Gene expression technique

ABSTRACT

The present invention provides a method for producing a desired protein (such as a desired heterologous protein) comprising:
     (a) providing a host cell comprising a first recombinant gene encoding a protein comprising the sequence of a first chaperone protein, a second recombinant gene encoding a protein comprising the sequence of a second chaperone protein and a third gene, such as a third recombinant gene, encoding a desired protein (such as a desired heterologous protein), wherein the first and second chaperones are different; and   (b) culturing the host cell in a culture medium to obtain expression of the first, second and third genes.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.13/474,313 filed on May 17, 2012, now allowed, which is a divisional ofU.S. patent application Ser. No. 11/722,539 filed Jun. 22, 2007,pending, which is a National Stage application based on InternationalApplication No. PCT/GB2005/005085, filed Dec. 23, 2005, which is acontinuation-in-part of International Application Nos. PCT/GB2004/005435and PCT/GB2004/005462, both of which were filed on Dec. 23, 2004 andboth of which claim priority to United Kingdom Application Nos.0329722.3 and 0329681.1, both filed Dec. 23, 2003, the disclosures ofwhich are incorporated herein by reference.

FIELD OF THE INVENTION

The present application relates to gene expression techniques.

BACKGROUND OF THE INVENTION

The listing or discussion of a prior-published document in thisspecification should not necessarily be taken as an acknowledgement thatthe document is part of the state of the art or is common generalknowledge.

The class of proteins known as chaperones has been defined by Hartl(1996, Nature, 381, 571-580) as a protein that binds to and stabilisesan otherwise unstable conformer of another protein and, by controlledbinding and release, facilitates its correct fate in vivo, be itfolding, oligomeric assembly, transport to a particular subcellularcompartment, or disposal by degradation.

BiP (also known as GRP78, Ig heavy chain binding protein and Kar2p inyeast) is an abundant ˜70 kDa chaperone of the hsp 70 family, residentin the endoplasmic reticulum (ER), which amongst other functions, servesto assist in transport in the secretory system and fold proteins.

Protein disulphide isomerase (PDI) is a chaperone protein, resident inthe ER that is involved in the catalysis of disulphide bond formationduring the post-translational processing of proteins.

Studies of the secretion of both native and foreign proteins have shownthat transit from the ER to the Golgi is the rate-limiting step.Evidence points to a transient association of the BiP with normalproteins and a more stable interaction with mutant or misfolded forms ofa protein. As a result, BiP may play a dual role in solubilising foldingprecursors and preventing the transport of unfolded and unassembledproteins. Robinson and Wittrup, 1995, Biotechnol. Prog. 11, 171-177,have examined the effect of foreign protein secretion on BiP (Kar2p) andPDI protein levels in Saccharomyces cerevisiae and found that prolongedconstitutive expression of foreign secreted proteins reduces soluble BiPand PDI to levels undetectable by Western analysis. The lowering of ERchaperone and foldase levels as a consequence of heterologous proteinsecretion has important implications for attempts to improve yeastexpression/secretion systems.

Expression of chaperones is regulated by a number of mechanisms,including the unfolded protein response (UPR).

Using recombinant techniques, multiple PDI gene copies have been shownto increase PDI protein levels in a host cell (Farquhar et al, 1991,Gene, 108, 81-89).

Co-expression of the gene encoding PDI and a gene encoding aheterologous disulphide-bonded protein was first suggested in WO93/25676, published on 23 December 1993, as a means of increasing theproduction of the heterologous protein. WO 93/25676 reports that therecombinant expression of antistasin and tick anticoagulant protein canbe increased by co-expression with PDI.

This strategy has been exploited to increase the recombinant expressionof other types of protein.

Robinson et al, 1994, Bio/Technology, 12, 381-384 reported that arecombinant additional PDI gene copy in Saccharomyces cerevisiae couldbe used to increase the recombinant expression of human platelet derivedgrowth factor (PDGF) B homodimer by ten-fold and Schizosacharomycespombe acid phosphatase by four-fold.

Hayano et al, 1995, FEBS Letters, 377, 505-511 described theco-expression of human lysozyme and PDI in yeast. Increases of around30-60% in functional lysozyme production and secretion were observed.

Shusta et al, 1998, Nature Biotechnology, 16, 773-777 reported that therecombinant expression of single-chain antibody fragments (scFv) inSaccharomyces cerevisiae could be increased by between 2-8 fold byover-expressing PDI in the host cell.

Bao & Fukuhara, 2001, Gene, 272, 103-110 reported that the expressionand secretion of recombinant human serum albumin (rHSA) in the yeastKluyveromyces lactis could be increased by 15-fold or more byco-expression with an additional recombinant copy of the yeast PDI gene(KlPDI1).

In order to produce co-transformed yeast comprising both a PDI gene anda gene for a heterologous protein, WO 93/25676 taught that the two genescould be chromosomally integrated; one could be chromosomally integratedand one present on a plasmid; each gene could be introduced on adifferent plasmid; or both genes could be introduced on the sameplasmid. WO 93/25676 exemplified expression of antistasin from theplasmid pKH4α2 in yeast strains having a chromosomally integratedadditional copy of a PDI gene (Examples 16 and 17); expression ofantistasin from the vector K991 with an additional PDI gene copy beingpresent on a multicopy yeast shuttle vector named YEp24 (Botstein et al,1979, Gene, 8, 17-24) (Example 20); and expression of both theantistasin and the PDI genes from the yeast shuttle vector pC1/1(Rosenberg et al, 1984, Nature, 312, 77-80) under control of the GAL10and GAL1 promoters, respectively. Indeed, Robinson and Wittrup, 1995,op. cit., also used the GAL1-GAL10 intergenic region to expresserythropoietin and concluded that production yeast strains for thesecretion of heterologous proteins should be constructed using tightlyrepressible, inducible promoters, otherwise the negative effects ofsustained secretion (i.e. lowered detectable BiP and PDI) would bedominant after the many generations of cell growth required to fill alarge-scale fermenter.

Subsequent work in the field has identified chromosomal integration oftransgenes as the key to maximising recombinant protein production.

-   Robinson et al, 1994, op. cit., obtained the observed increases in    expression of PDGF and S. pombe acid phosphatase using an additional    chromosomally integrated PDI gene copy. Robinson et at reported that    attempts to use the multi-copy 2 μm expression vector to increase    PDI protein levels had had a detrimental effect on heterologous    protein secretion.-   Hayano et al, 1995, op. cit. described the introduction of genes for    human lysozyme and PDI into a yeast host each on a separate    linearised integration vector, thereby to bring about chromosomal    integration.-   Shusta et al, 1998, op. cit., reported that in yeast systems, the    choice between integration of a transgene into the host chromosome    versus the use of episomal expression vectors can greatly affect    secretion and, with reference to Parekh & Wittrup, 1997, Biotechnol.    Prog., 13, 117-122, that stable integration of the scFv gene into    the host chromosome using a 6 integration vector was superior to the    use of a 2 μm-based expression plasmid. Parekh & Wittrup, op. cit.,    had previously taught that the expression of bovine pancreatic    trypsin inhibitor (BPTI) was increased by an order of magnitude    using a 6 integration vector rather than a 2 μm-based expression    plasmid. The 2 μm-based expression plasmid was said to be    counter-productive for the production of heterologous secreted    protein.-   Bao & Fukuhara, 2001, op. cit., reported that “It was first thought    that the KlPDI1 gene might be directly introduced into the    multi-copy vector that carried the rHSA expression cassette.    However, such constructs were found to severely affect yeast growth    and plasmid stability. This confirmed our previous finding that the    KlPDI1 gene on a multi-copy vector was detrimental to growth of K.    lactis cells (Bao et al, 2000)”. Bao et al, 2000, Yeast, 16,    329-341, as referred to in the above-quoted passage of Bao &    Fukuhara, reported that the KlPDI1 gene had been introduced into K.    lactis on a multi-copy plasmid, pKan707, and that the presence of    the plasmid caused the strain to grow poorly. Bao et at concluded    that over-expression of the KlPDI1 gene was toxic to K. lactis    cells. In the light of the earlier findings in Bao et al, Bao &    Fukuhara chose to introduce a single duplication of KlPDI1 on the    host chromosome.

Against this background, we had previously surprisingly demonstratedthat, contrary to the suggestions in the prior art, when the genes for achaperone protein and a heterologous protein are co-expressed on a 2μm-family multi-copy plasmid in yeast, the production of theheterologous protein is substantially increased.

Our earlier application, which has been published as WO 2005/061718,from which this application claims priority, disclosed a method forproducing heterologous protein comprising:

-   -   (a) providing a host cell comprising a 2 μm-family plasmid, the        plasmid comprising a gene encoding a protein comprising the        sequence of a chaperone protein and a gene encoding a        heterologous protein;    -   (b) culturing the host cell in a culture medium under conditions        that allow the expression of the gene encoding the chaperone        protein and the gene encoding a heterologous protein;    -   (c) purifying the thus expressed heterologous protein from the        culture medium; and    -   (d) optionally, lyophilising the thus purified protein.

As discussed above, Bao et al, 2000, Yeast, 16, 329-341 reported thatover-expression of the K. lactis PDI gene KlPDI1 was toxic to K. lactiscells. Against this background we have surprisingly found that, not onlyis it possible to over-express PDI and other chaperones without thedetrimental effects reported in Bao et al, but that two differentchaperones can be recombinantly over-expressed in the same cell and,rather than being toxic, can increase the expression of proteins,including heterologous proteins, to levels higher than the levelsobtained by individual expression of either of the chaperones. This wasnot expected. On the contrary, in light of the teaching of Bao et al,one would think that over-expression of two chaperones would be evenmore toxic than the over-expression of one. Moreover, in light of someinitial findings which are also reported below in the presentapplication, it was expected that the increases in heterologous proteinexpression obtained by co-expression with a single chaperone would be atthe maximum level possible for the cell system used. Therefore, it wasparticularly surprising to find that yet further increases in proteinexpression could be obtained by co-expression of two differentchaperones with the protein.

SUMMARY OF THE INVENTION

Accordingly, as a first aspect of the present invention there isprovided a method for producing a desired protein, such as aheterologous protein, comprising providing a host cell comprising afirst recombinant gene encoding a protein comprising the sequence of afirst chaperone protein, a second recombinant gene encoding a proteincomprising the sequence of a second chaperone protein and a third gene(optionally the third gene being recombinant) encoding the desiredprotein (optionally a heterologous protein), wherein the first andsecond chaperones are different; and culturing the host cell in aculture medium under conditions that allow the expression of the first,second and third genes.

Optionally the thus expressed desired protein may, or may not, bepurified from the cultured host cell or the culture medium.

Optionally, the thus purified desired protein may, or may not, belyophilised.

The method may, or may not, further comprise the step of formulating thepurified desired protein with a carrier or diluent and optionallypresenting the thus formulated protein in a unit dosage form, in themanner discussed above.

The term “recombinant gene” includes nucleic acid sequences that operateindependently as “stand alone” expressible sequences to produce anencoded protein or, in the alternative, nucleic acid sequencesintroduced that operate in combination with endogenous sequences (suchas by integration into an endogenous sequence so as to produce a nucleicacid sequence that is different to the endogenous sequence) within thehost to cause increased expression of a target protein.

A “recombinant gene” is typically a gene that is not naturally found inthe context used. For example, a gene that is integrated, at anintegration site, into the chromosome of a host organism can be said tobe a “recombinant gene” if it comprises a sequence that does notnaturally occur at the integration site. Thus, the “recombinant gene”may, or may not, comprise a non-natural sequence in the coding,regulatory or any other region of the gene, or may, or may not, comprisethe sequence of a naturally occurring gene but be introduced into thechromosome of a host organism at an integration site at which thatsequence does not naturally occur. The same issues apply, mutatismutandis, to the insertion of a “recombinant gene” into a plasmid.

The terms “chromosomally integrated” and “integrated into the chromosomeof the host cell” are well recognised terms of the art. For avoidance ofdoubt, these terms include the integration of polynucleotide sequencesin any inheritable nuclear material that naturally occurs in a hostcell, other than for naturally occurring plasmids. Thus, apolynucleotide sequence that is “integrated into the chromosome of thehost cell” may, or may not, be integrated into the chromosome of aprocaryotic (such as a bacterial) cell, or into any part of the genomeof a eucaryotic cell, such as into nuclear genetic material includingthe chromosome (or, one of the chromosomes), the mitochondrial genome orthe chloroplast genome.

The first and second chaperones may, or may not, each individually, beone of the specifically listed chaperones as discussed below, and are acombination of chaperones that, when co-expressed in the same host cell,provide at least an additive effect to the increase in expression of thedesired protein. By “additive effect” we mean that the level ofexpression of the desired protein in the host cell is higher when thefirst and second recombinant genes are simultaneously co-expressed withthe third gene as compared to the same system wherein (i) the firstrecombinant gene is co-expressed with the third gene in the absence ofthe expression of the second recombinant gene and (ii) the secondrecombinant gene is co-expressed with the third gene in the absence ofthe expression of the first recombinant gene.

The term “chaperone” as used herein refers to a protein that binds toand stabilises an otherwise unstable conformer of another protein, andby controlled binding and release, facilitates its correct fate in vivo,be it folding, oligomeric assembly, transport to a particularsubcellular compartment, or disposal by degradation. Accordingly achaperone is also a protein that is involved in protein folding, orwhich has chaperone activity or is involved in the unfolded proteinresponse. Chaperone proteins of this type are known in the art, see forexample the Stanford Genome Database (SGD), which can be found on theworld wide web at www.yeastgenome.org. Preferred chaperones areeucaryotic chaperones, especially preferred chaperones are yeastchaperones, including AHA1, CCT2, CCT3, CCT4, CCT5, CCT6, CCT7, CCT8,CNS1, CPR3, CPR6, ERO1, EUG1, FMO1, HCH1, HSP10, HSP12, HSP104, HSP26,HSP30, HSP42, HSP60, HSP78, HSP82, JEM1, MDJ1, MDJ2, MPD1, MPD2, PDI1,PFD1, ABC1, APJ1, ATP11, ATP12, BTT1, CDC37, CPR7, HSC82, KAR2, LHS1,MGE1, MRS11, NOB1, ECM10, SSA1, SSA2, SSA3, SSA4, SSC1, SSE2, SIL1,SLS1, ORM1, ORM2, PER1, PTC2, PSE1, UBI4 and HAC1 or a truncatedintronless HAC1 (Valkonen et al. 2003, Applied Environ. Micro., 69,2065), as well as TIM9, PAM18 (also known as TIM14) and TCP1 (also knownas CCT1).

A chaperone useful in the practice of the present invention may, or maynot, be:

-   -   a heat shock protein, such as a protein that is a member of the        hsp70 family of proteins (including Kar2p, SSA and SSB proteins,        for example proteins encoded by SSA1, SSA2, SSA3, SSA4, SSB1 and        SSB2), a protein that is a member of the HSP90-family, or a        protein that is a member of the HSP40-family or proteins        involved in their modulation (e.g. Sil1p), including DNA-J and        DNA-J-like proteins (e.g. Jem1p, Mdj2p);    -   a protein that is a member of the karyopherin/importin family of        proteins, such as the alpha or beta families of        karyopherin/importin proteins, for example the karyopherin beta        protein PSE1;    -   a protein that is a member of the ORMDL family described by        Hjelmqvist et al, 2002, Genome Biology, 3(6),        research0027.1-0027.16, such as Orm2p.    -   a protein that is naturally located in the endoplasmic reticulum        or elsewhere in the secretory pathway, such as the golgi. For        example, a protein that naturally acts in the lumen of the        endoplasmic reticulum (ER), particularly in secretory cells.        such as PDI    -   a protein that is transmembrane protein anchored in the ER, such        as a member of the ORMDL family described by Hjelmqvist et al,        2002, supra, (for example, Orm2p);    -   a protein that acts in the cytosol, such as the hsp70 proteins,        including SSA and SSB proteins, for example protein production        SSA1, SSA2, SSA3, SSA4, SSB1 and SSB2;    -   a protein that acts in the nucleus, the nuclear envelope and/or        the cytoplasm, such as Pse1p;    -   a protein that is “essential” to the viability of the cell, such        as PDI, or a protein encoded by one of the following genes:        CCT2, CCT3, CCT4, CCT5, CCT6, CCT7, CCT8, CNS1, ERO1, HSP10,        HSP60, PDI1, CDC37, KAR2, MGE1, MRS11, NOB1, SSC1, TIM9, PAM18        and TCP1, or a protein that is an essential karyopherin protein,        such as Pse1p;    -   a protein that is involved in sulphydryl oxidation or disulphide        bond formation, breakage or isomerization, or a protein that        catalyses thiol:disulphide interchange reactions in proteins,        particularly during the biosynthesis of secretory and cell        surface proteins, such as protein disulphide isomerases (e.g.        Pdi1p, Mpd1p), homologues (e.g. Eug1p) and/or related proteins        (e.g. Mpd2p, Fmo1p, Ero1p);    -   a protein that is involved in protein synthesis, assembly or        folding, such as PDI and Ssa1p;    -   a protein that binds preferentially or exclusively to unfolded,        rather than mature protein, such as the hsp70 proteins,        including SSA and SSB proteins, for example proteins encoded by        SSA1, SSA2, SSA3, SSA4, SSB1 and SSB2;    -   a protein that prevents aggregation of precursor proteins in the        cytosol, such as the hsp70 proteins, including SSA and SSB        proteins, for example proteins encoded by SSA1, SSA2, SSA3,        SSA4, SSB1 and SSB2;    -   a protein that binds to and stabilises damaged proteins, for        example Ssa1p;    -   a protein that is involved in the unfolded protein response or        provides for increased resistance to agents (such as tunicamycin        and dithiothreitol) that induce the unfolded protein response,        such as a member of the ORMDL family described by Hjelmqvist et        al, 2002, supra (for example, Orm2p) or proteins involved in the        response to stress (e.g. Ubi4p);    -   a protein that is a co-chaperone and/or a protein indirectly        involved in protein folding and/or the unfolded protein response        (e.g. hsp104p, Mdj1p);    -   a protein that is involved in the nucleocytoplasmic transport of        macromolecules, such as Pse1p;    -   a protein that mediates the transport of macromolecules across        the nuclear membrane by recognising nuclear location sequences        and nuclear export sequences and interacting with the nuclear        pore complex, such as PSE1;    -   a protein that is able to reactivate ribonuclease activity        against RNA of scrambled ribonuclease as described in as        described in EP 0 746 611 and Hillson et al, 1984, Methods        Enzymol., 107, 281-292, such as PDI;    -   a protein that has an acidic pI (for example, 4.0-4.5), such as        PDI;    -   a protein that is a member of the Hsp70 family, and optionally        possesses an N-terminal ATP-binding domain and a C-terminal        peptide-binding domain, such as Ssa1p.    -   a protein that is a peptidyl-prolyl cis-trans isomerases (e.g.        Cpr3p, Cpr6p);    -   a protein that is a homologue of known chaperones (e.g. Hsp10p);    -   a protein that is a mitochondrial chaperone (e.g. Cpr3p);    -   a protein that is a cytoplasmic or nuclear chaperone (e.g.        Cns1p);    -   a protein that is a membrane-bound chaperone (e.g. Orm2p,        Fmo1p);    -   a protein that has chaperone activator activity or chaperone        regulatory activity (e.g. Aha1p, Hac1p, Hch1p);    -   a protein that transiently binds to polypeptides in their        immature form to cause proper folding transportation and/or        secretion, including proteins required for efficient        translocation into the endoplasmic reticulum (e.g. Lhs1p) or        their site of action within the cell (e.g. Pse1p);    -   a protein that is a involved in protein complex assembly and/or        ribosome assembly (e.g. Atp11p, Pse1p, Nob1p);    -   a protein of the chaperonin T-complex (e.g. Cct2p);    -   a protein of the prefoldin complex (e.g. Pfd1p);    -   a mitochondrial intermembrane space protein such as Tim9p;    -   a protein that can form a complex, in vivo, with Mrs11p/Tim10p,        such as Tim9p;    -   a protein that is involved in the mediation of import and        insertion of polytopic inner membrane proteins, such as Tim9p;    -   a protein that can prevent the aggregation of incoming proteins,        such as Tim9p;    -   a protein that can be a functional constituent of the        mitochondrial import motor associated with presequence        translocase (along with Ssc1p, Tim44p, Mge1p and Pam16p) such as        Pam18p;    -   a protein that can stimulate the ATPase activity of Ssc1p, such        as to drive mitochondrial import, such as Pam18p;    -   a protein that contains a J domain, such as Pam18p;    -   a protein that can act as an alpha subunit of        chaperonin-containing T-complex, which mediates protein folding        in the cytosol, such as Tcp1p;    -   a protein that can play a role in the in maintenance of an actin        cytoskeleton, such as Tcp1p; or    -   a protein that is, or is a homolog to, a Drosophila melanogaster        or mouse tailless complex polypeptide, such as Tcp1p.

A preferred chaperone is protein disulphide isomerase (PDI) or afragment or variant thereof having an equivalent ability to catalyse theformation of disulphide bonds within the lumen of the endoplasmicreticulum (ER). By “PDI” we include any protein having the ability toreactivate the ribonuclease activity against RNA of scrambledribonuclease as described in EP 0 746 611 and Hillson et al, 1984,Methods Enzymol., 107, 281-292.

PDI is an enzyme which typically catalyzes thiol:disulphide interchangereactions, and is a major resident protein component of the ER lumen insecretory cells. A body of evidence suggests that it plays a role insecretory protein biosynthesis (Freedman, 1984, Trends Biochem. Sci., 9,438-41) and this is supported by direct cross-linking studies in situ(Roth and Pierce, 1987, Biochemistry, 26, 4179-82). The finding thatmicrosomal membranes deficient in PDI show a specific defect incotranslational protein disulphide (Bulleid and Freedman, 1988, Nature,335, 649-51) implies that the enzyme functions as a catalyst of nativedisulphide bond formation during the biosynthesis of secretory and cellsurface proteins. This role is consistent with what is known of theenzyme's catalytic properties in vitro; it catalyzes thiol: disulphideinterchange reactions leading to net protein disulphide formation,breakage or isomerization, and can typically catalyze protein foldingand the formation of native disulphide bonds in a wide variety ofreduced, unfolded protein substrates (Freedman et al., 1989, Biochem.Soc. Symp., 55, 167-192). PDI also functions as a chaperone since mutantPDI lacking isomerase activity accelerates protein folding (Hayano etal, 1995, FEBS Letters, 377, 505-511). Recently, sulphydryl oxidation,not disulphide isomerisation was reported to be the principal functionof Protein Disulphide Isomerase in S. cerevisiae (Solovyov et al., 2004,J. Biol. Chem., 279 (33) 34095-34100). The DNA and amino acid sequenceof the enzyme is known for several species (Scherens et al, 1991, Yeast,7, 185-193; Farquhar et al, 1991, Gene, 108, 81-89; EP074661; EP0293793;EP0509841) and there is increasing information on the mechanism ofaction of the enzyme purified to homogeneity from mammalian liver(Creighton et al, 1980, J. Mol. Biol., 142, 43-62; Freedman et al, 1988,Biochem. Soc. Trans., 16, 96-9; Gilbert, 1989, Biochemistry, 28,7298-7305; Lundstrom and Holmgren, 1990, J. Biol. Chem., 265, 9114-9120;Hawkins and Freedman, 1990, Biochem. J., 275, 335-339). Of the manyprotein factors currently implicated as mediators of protein folding,assembly and translocation in the cell (Rothman, 1989, Cell, 59,591-601), PDI has a well-defined catalytic activity.

The deletion or inactivation of the endogenous PDI gene in a hostresults in the production of an inviable host. In other words, theendogenous PDI gene is an “essential” gene.

PDI is readily isolated from mammalian tissues and the homogeneousenzyme is a homodimer (2×57 kD) with characteristically acidic pI(4.0-4.5) (Hillson et al, 1984, op. cit.). The enzyme has also beenpurified from wheat and from the alga Chlamydomonas reinhardii (Kaska etal, 1990, Biochem. J., 268, 63-68), rat (Edman et al, 1985, Nature, 317,267-270), bovine (Yamauchi et al, 1987, Biochem. Biophys. Res. Comm.,146, 1485-1492), human (Pihlajaniemi et al, 1987, EMBO J., 6, 643-9),yeast (Scherens et al, supra; Farquhar et al, op. cit.) and chick(Parkkonen et al, 1988, Biochem. J., 256, 1005-1011). The proteins fromthese vertebrate species show a high degree of sequence conservationthroughout and all show several overall features first noted in the ratPDI sequence (Edman et al., 1985, op. cit.).

Preferred PDI sequences include those from humans and those from yeastspecies, such as S. cerevisiae.

A yeast protein disulphide isomerase precursor, PDI1, can be found asGenbank accession no. CAA42373 or BAA00723 and has a sequence of 522amino acids as described in WO 2005/061718, the contents of which areincorporated herein by reference.

An alternative yeast protein disulphide isomerase sequence can be foundas Genbank accession no. CAA38402, which has a sequence of 530 aminoacids as described in WO 2005/061718, the contents of which areincorporated herein by reference.

The alignment of these sequences (the sequence of Genbank accession no.CAA42373 or BAA00723 first, the sequence of Genbank accession no.CAA38402 second) in WO 2005/061718, the contents of which areincorporated herein by reference, shows that the differences betweenthese two sequences are a single amino acid difference at position 114(highlighted in bold) and that the sequence defined by Genbank accessionno. CAA38402 contains the additional amino acids EADAEAEA at positions506-513.

Variants and fragments of the above PDI sequences, and variants of othernaturally occurring PDI sequences are also included in the presentinvention. A “variant”, in the context of PDI, refers to a proteinwherein at one or more positions there have been amino acid insertions,deletions, or substitutions, either conservative or non-conservative,provided that such changes result in a protein whose basic properties,for example enzymatic activity (type of and specific activity),thermostability, activity in a certain pH-range (pH-stability) have notsignificantly been changed.

“Significantly” in this context means that one skilled in the art wouldsay that the properties of the variant may, or may not, still bedifferent but would not be unobvious over the ones of the originalprotein.

By “conservative substitutions” is intended combinations such as Val,Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg,His; and Phe, Tyr, Trp. Preferred conservative substitutions includeGly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; andPhe, Tyr.

A “variant” typically has at least 25%, at least 50%, at least 60% or atleast 70%, preferably at least 80%, more preferably at least 90%, evenmore preferably at least 95%, yet more preferably at least 99%, mostpreferably at least 99.5% sequence identity to the polypeptide fromwhich it is derived.

The percent sequence identity between two polypeptides may be determinedusing suitable computer programs, as discussed below. Such variants may,or may not, be natural or made using the methods of protein engineeringand site-directed mutagenesis as are well known in the art.

A “fragment”, in the context of PDI, refers to a protein wherein at oneor more positions there have been deletions. Thus the fragment may, ormay not, comprise at most 5, 10, 20, 30, 40 or 50%, typically up to 60%,more typically up to 70%, preferably up to 80%, more preferably up to90%, even more preferably up to 95%, yet more preferably up to 99% ofthe complete sequence of the full mature PDI protein. Particularlypreferred fragments of PDI protein comprise one or more whole domains ofthe desired protein.

A fragment or variant of PDI may, or may not, be a protein that, whenexpressed recombinantly in a host cell, can complement the deletion ofthe endogenously encoded PDI gene in the host cell, such as S.cerevisiae, and may, or may not, for example, be a naturally occurringhomolog of PDI, such as a homolog encoded by another organism, such asanother yeast or other fungi, or another eucaryote such as a human orother vertebrate, or animal or by a plant.

Where the first chaperone is PDI, particularly mammalian or yeast PDI,then in one embodiment the second chaperone is not an hsp70 chaperoneprotein (such as yeast KAR2, HSP70, BiP, SSA1-4, SSB1, SSC1, SSD1 or aeucaryotic hsp70 protein such as HSP68, HSP72, HSP73, HSC70, clathrinuncoating ATPase, IgG heavy chain binding protein (BiP),glucose-regulated proteins 75, 78 and 80 (GPR75, GRP78 and GRP80) andthe like). Specifically in one embodiment the first chaperone is notyeast PDI when the second chaperone is yeast KAR2. Specifically inanother embodiment the first chaperone is not mammalian PDI when thesecond chaperone is mammalian BiP.

Alternatively, where the first and second chaperones are, for example,PDI, particularly mammalian or yeast PDI, and an hsp70 chaperone proteinas described above, respectively, then the desired protein may be aheterologous protein that may or may not be a protein selected from—

-   -   mammalian gene products such as enzymes, cytokines, growth        factors, hormones, vaccines, antibodies and the like;        erythropoietin, insulin, somatotropin, growth hormone releasing        factor, platelet derived growth factor, epidermal growth factor,        transforming growth factor α, transforming growth factor β,        epidermal growth factor, fibroblast growth factor, nerve growth        factor, insulin-like growth factor I, insulin-like growth factor        II, clotting Factor VIII, superoxide dismutase, α-interferon,        γ-interferon, interleukin-1, interleukin-2, interleukin-3,        interleukin-4, interleukin-5, interleukin-6, granulocyte colony        stimulating factor, multi-lineage colony stimulating activity,        granulocyte-macrophage stimulating factor, macrophage colony        stimulating factor, T cell growth factor, lymphotoxin and the        like; or human gene products;    -   any gene product which can be used as a vaccine, including any        structural, membrane-associated, membrane-bound or secreted gene        product of a mammalian pathogen, including viruses, bacteria,        single-celled or multi-celled parasites which can infect or        attack a mammal, in particular viruses such as human        immunodeficiency virus (HIV), R. rickettsii, vaccinia, Shigella,        poliovirus, adenovirus, influenza, hepatitis A, hepatitis B,        dengue virus, Japanese B encephalitis, Varicella zoster,        cytomegalovirus, hepatitis A, rotavirus, as well as vaccines        against viral diseases like Lyme disease, measles, yellow fever,        mumps, rabies, herpes, influenza, parainfluenza and the like; or        bacteria such as Vibrio cholerae, Salmonella typhi, Bordetella        pertussis, Streptococcus pneumoniae, Hemophilus influenza,        Clostridium tetani, Corynebacterium diphtheriae, Mycobacterium        leprae, Neisseriaqonorrhoeae, Neisseriameningitidis,        Coccidioides immitis and the like.

Another preferred chaperone is a protein comprising the sequence of aprotein encoded by the gene SSA1, or a fragment or variant thereofhaving an equivalent chaperone-like activity. SSA1, also known as YG100,is located on chromosome I of the S. cerevisiae genome and is 1.93-kbpin size.

One published protein sequence of the protein encoded by the gene SSA1is as described in WO 2005/061718, the contents of which areincorporated herein by reference.

A published coding sequence for SSA1 is also described in WO2005/061718, the contents of which are incorporated herein by reference,although it will be appreciated that the sequence can be modified bydegenerate substitutions to obtain alternative nucleotide sequenceswhich encode an identical protein product.

The protein Ssa1p belongs to the Hsp70 family of proteins and isresident in the cytosol. Hsp70s possess the ability to perform a numberof chaperone activities; aiding protein synthesis, assembly and folding;mediating translocation of polypeptides to various intracellularlocations, and resolution of protein aggregates (Becker & Craig, 1994,Eur. J. Biochem. 219, 11-23). Hsp70 genes are highly conserved,possessing an N-terminal ATP-binding domain and a C-terminalpeptide-binding domain. Hsp70 proteins interact with the peptidebackbone of, mainly unfolded, proteins. The binding and release ofpeptides by hsp70 proteins is an ATP-dependent process and accompaniedby a conformational change in the hsp70 (Becker & Craig, 1994, supra).

Cytosolic hsp70 proteins are particularly involved in the synthesis,folding and secretion of proteins (Becker & Craig, 1994, supra). In S.cerevisiae cytosolic hsp70 proteins have been divided into two groups;SSA (SSA 1-4) and SSB (SSB 1 and 2) proteins, which are functionallydistinct from each other. The SSA family is “essential” in that at leastone protein from the group must be active to maintain cell viability(Becker & Craig, 1994, supra). Cytosolic hsp70 proteins bindpreferentially to unfolded and not mature proteins. This suggests thatthey prevent the aggregation of precursor proteins, by maintaining themin an unfolded state prior to being assembled into multimolecularcomplexes in the cytosol and/or facilitating their translocation tovarious organelles (Becker & Craig, 1994, supra). SSA proteins areparticularly involved in posttranslational biogenesis and maintenance ofprecursors for translocation into the endoplasmic reticulum andmitochondria (Kim et al., 1998, Proc. Natl. Acad. Sci. USA. 95,12860-12865; Ngosuwan et al., 2003, J. Biol. Chem. 278 (9), 7034-7042).Ssa1p has been shown to bind damaged proteins, stabilising them in apartially unfolded form and allowing refolding or degradation to occur(Becker & Craig, 1994, supra; Glover & Lindquist, 1998, Cell. 94,73-82).

Demolder et al, 1994, J. Biotechnol., 32, 179-189 reported thatover-expression of SSA1 in yeast provided for increases in theexpression of a recombinant chromosomally integrated gene encoding humaninterferon-β. There is no suggestion that increases in heterologous geneexpression could be achieved if SSA1 and human interferon-β were to beencoded by recombinant genes on the same plasmid. In fact, in light ofmore recent developments in the field of over-expression of chaperonesin yeast (e.g. Robinson et al, 1994, op. cit.; Hayano et al, 1995, op.cit.; Shusta et al, 1998, op. cit; Parekh & Wittrup, 1997, op. cit.; Bao& Fukuhara, 2001, op. cit.; and Bao et al, 2000, op. cit) the skilledperson would have been disinclined to express SSA1 from a 2 μm-familyplasmid at all, much less to express both SSA1 and a heterologousprotein from a 2 μm-family plasmid in order to increase the expressionlevels of a heterologous protein.

Variants and fragments of is a protein comprising the sequence of aprotein encoded by the gene SSA1 are also included in the presentinvention. A “variant”, in the context of a protein encoded by the geneSSA1, refers to a protein having the sequence of native Ssa1p other thanat one or more positions where there have been amino acid insertions,deletions, or substitutions, either conservative or non-conservative,provided that such changes result in a protein whose basic properties,for example enzymatic activity (type of and specific activity),thermostability, activity in a certain pH-range (pH-stability) have notsignificantly been changed. “Significantly” in this context means thatone skilled in the art would say that the properties of the variant maystill be different but would not be unobvious over the ones of theoriginal protein.

By “conservative substitutions” is intended combinations such as Val,Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg,His; and Phe, Tyr, Trp. Preferred conservative substitutions includeGly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; andPhe, Tyr.

A “variant” of Ssa1p typically has at least 25%, at least 50%, at least60% or at least 70%, preferably at least 80%, more preferably at least90%, even more preferably at least 95%, yet more preferably at least99%, most preferably at least 99.5% sequence identity to the sequence ofnative Ssa1p.

The percent sequence identity between two polypeptides may be determinedusing suitable computer programs, as discussed below. Such variants may,or may not, be natural or made using the methods of protein engineeringand site-directed mutagenesis as are well known in the art.

A “fragment”, in the context of Ssa1p, refers to a protein having thesequence of native Ssa1p other than for at one or more positions wherethere have been deletions. Thus the fragment may, or may not, compriseat most 5, 10, 20, 30, 40 or 50%, typically up to 60%, more typically upto 70%, preferably up to 80%, more preferably up to 90%, even morepreferably up to 95%, yet more preferably up to 99% of the completesequence of the full mature Ssa1p protein. Particularly preferredfragments of SSA1 protein comprise one or more whole domains of thedesired protein.

A fragment or variant of Ssa1p may, or may not, be a protein that, whenexpressed recombinantly in a host cell, such as S. cerevisiae, cancomplement the deletion of the endogenously encoded SSA1 gene (orhomolog thereof) in the host cell and may, or may not, for example, be anaturally occurring homolog of Ssa1p, such as a homolog encoded byanother organism, such as another yeast or other fungi, or anothereucaryote such as a human or other vertebrate, or animal or by a plant.

Another preferred chaperone is protein comprising the sequence of aprotein encoded by the PSE1 gene, or a fragment or variant thereofhaving equivalent chaperone-like activity.

PSE1, also known as KAP121, is an essential gene, located on chromosomeXIII.

A published protein sequence for the protein Pse1p is as described in WO2005/061718, the contents of which are incorporated herein by reference.

A published nucleotide coding sequence of PSE1 is also described in WO2005/061718, the contents of which are incorporated herein by reference,although it will be appreciated that the sequence can be modified bydegenerate substitutions to obtain alternative nucleotide sequenceswhich encode an identical protein product.

The PSE1 gene is 3.25-kbp in size. Pse1p is involved in thenucleocytoplasmic transport of macromolecules (Seedorf & Silver, 1997,Proc. Natl. Acad. Sci. USA. 94, 8590-8595). This process occurs via thenuclear pore complex (NPC) embedded in the nuclear envelope and made upof nucleoporins (Ryan & Wente, 2000, Curr. Opin. Cell Biol. 12,361-371). Proteins possess specific sequences that contain theinformation required for nuclear import, nuclear localisation sequence(NLS) and export, nuclear export sequence (NES) (Pemberton et al., 1998,Curr. Opin. Cell Biol. 10, 392-399). Pse1p is a karyopherin/importin, agroup of proteins, which have been divided up into α and β families.Karyopherins are soluble transport factors that mediate the transport ofmacromolecules across the nuclear membrane by recognising NLS and NES,and interact with and the NPC (Seedorf & Silver, 1997, supra; Pembertonet al., 1998, supra; Ryan & Wente, 2000, supra). Translocation throughthe nuclear pore is driven by GTP hydrolysis, catalysed by the smallGTP-binding protein, Ran (Seedorf & Silver, 1997, supra). Pse1p has beenidentified as a karyopherin β. 14 karyopherin β proteins have beenidentified in S. cerevisiae, of which only 4 are “essential”. This isperhaps because multiple karyopherins may mediate the transport of asingle macromolecule (Isoyama et al., 2001, J. Biol. Chem. 276 (24),21863-21869). Pse1p is localised to the nucleus, at the nuclearenvelope, and to a certain extent to the cytoplasm. This suggests theprotein moves in and out of the nucleus as part of its transportfunction (Seedorf & Silver, 1997, supra). Pse1p is involved in thenuclear import of transcription factors (Isoyama et al., 2001, supra;Ueta et al., 2003, J. Biol. Chem. 278 (50), 50120-50127), histones(Mosammaparast et al., 2002, J. Biol. Chem. 277 (1), 862-868), andribosomal proteins prior to their assembly into ribosomes (Pemberton etal., 1998, supra). It also mediates the export of mRNA from the nucleus.Karyopherins recognise and bind distinct NES found on RNA-bindingproteins, which coat the RNA before it is exported from the nucleus(Seedorf & Silver, 1997, Pemberton et al., 1998, supra).

As nucleocytoplasmic transport of macromolecules is essential for properprogression through the cell cycle, nuclear transport factors, such asPse1p are novel candidate targets for growth control (Seedorf & Silver,1997, supra).

Overexpression of Pse1p (protein secretion enhancer) in S. cerevisiaehas also been shown to increase endogenous protein secretion levels of arepertoire of biologically active proteins (Chow et al., 1992; J. Cell.Sci. 101 (3), 709-719). There is no suggestion that increases inheterologous gene expression could be achieved if Pse1p and aheterologous protein were both to be encoded by recombinant genes on thesame plasmid. In fact, in light of more recent developments in theover-expression of chaperones in yeast (e.g. Robinson et al, 1994, op.cit.; Hayano et al, 1995, op. cit.; Shusta et al, 1998, op. cit; Parekh& Wittrup, 1997, op. cit.; Bao & Fukuhara, 2001, op. cit.; and Bao etal, 2000, op. cit) the skilled person would not have attempted toover-express a PSE1 gene from a 2 μm-family plasmid at all, much less toexpress both Pse1p and a heterologous protein from a 2 μm-family plasmidin order to increase the expression levels of a heterologous protein.

Variants and fragments of Pse1p are also included in the presentinvention. A “variant”, in the context of Pse1p, refers to a proteinhaving the sequence of native Pse1p other than for at one or morepositions where there have been amino acid insertions, deletions, orsubstitutions, either conservative or non-conservative, provided thatsuch changes result in a protein whose basic properties, for exampleenzymatic activity (type of and specific activity), thermostability,activity in a certain pH-range (pH-stability) have not significantlybeen changed. “Significantly” in this context means that one skilled inthe art would say that the properties of the variant may still bedifferent but would not be unobvious over the ones of the originalprotein.

By “conservative substitutions” is intended combinations such as Val,Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg,His; and Phe, Tyr, Trp. Preferred conservative substitutions includeGly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; andPhe, Tyr.

A “variant” of Pse1p typically has at least 25%, at least 50%, at least60% or at least 70%, preferably at least 80%, more preferably at least90%, even more preferably at least 95%, yet more preferably at least99%, most preferably at least 99.5% sequence identity to the sequence ofnative Pse1p.

The percent sequence identity between two polypeptides may be determinedusing suitable computer programs, as discussed below. Such variants may,or may not, be natural or made using the methods of protein engineeringand site-directed mutagenesis as are well known in the art.

A “fragment”, in the context of Pse1p, refers to a protein having thesequence of native Pse1p other than for at one or more positions wherethere have been deletions. Thus the fragment may, or may not, compriseat most 5, 10, 20, 30, 40 or 50%, typically up to 60%, more typically upto 70%, preferably up to 80%, more preferably up to 90%, even morepreferably up to 95%, yet more preferably up to 99% of the completesequence of the full mature Pse1p protein. Particularly preferredfragments of Pse1p protein comprise one or more whole domains of thedesired protein.

A fragment or variant of Pse1p may, or may not, be a protein that, whenexpressed recombinantly in a host cell, such as S. cerevisiae, cancomplement the deletion of the endogenous PSE1 gene in the host cell andmay, or may not, for example, be a naturally occurring homolog of Pse1p,such as a homolog encoded by another organism, such as another yeast orother fungi, or another eucaryote such as a human or other vertebrate,or animal or by a plant.

Another preferred chaperone is a protein comprising the sequence of aprotein encoded by the ORM2 gene, or a fragment or variant thereofhaving equivalent chaperone-like activity.

ORM2, also known as YLR350W, is located on chromosome XII (positions828729 to 829379) of the S. cerevisiae genome and encodes anevolutionarily conserved protein with similarity to the yeast proteinOrm1p. Hjelmqvist et al, 2002, Genome Biology, 3(6), research0027.1-0027.16 reports that ORM2 belongs to gene family comprising threehuman genes (ORMDL1, ORMDL2 and ORMDL3) as well as homologs inmicrosporidia, plants, Drosophila, urochordates and vertebrates. TheORMDL genes are reported to encode transmembrane proteins anchored inthe proteins endoplasmic reticulum (ER).

The protein Orm2p is required for resistance to agents that induce theunfolded protein response. Hjelmqvist et al, 2002 (supra) reported thata double knockout of the two S. cerevisiae ORMDL homologs (ORM1 andORM2) leads to a decreased growth rate and greater sensitivity totunicamycin and dithiothreitol.

One published sequence of Orm2p is as described in WO 2005/061718, thecontents of which are incorporated herein by reference.

The above protein is encoded in S. cerevisiae by the coding nucleotidesequence also as described in WO 2005/061718, the contents of which areincorporated herein by reference, although it will be appreciated thatthe sequence can be modified by degenerate substitutions to obtainalternative nucleotide sequences which encode an identical proteinproduct.

Variants and fragments of Orm2p are also included in the presentinvention. A “variant”, in the context of Orm2p, refers to a proteinhaving the sequence of native Orm2p other than for at one or morepositions where there have been amino acid insertions, deletions, orsubstitutions, either conservative or non-conservative, provided thatsuch changes result in a protein whose basic properties, for exampleenzymatic activity (type of and specific activity), thermostability,activity in a certain pH-range (pH-stability) have not significantlybeen changed. “Significantly” in this context means that one skilled inthe art would say that the properties of the variant may still bedifferent but would not be unobvious over the ones of the originalprotein.

By “conservative substitutions” is intended combinations such as Val,Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg,His; and Phe, Tyr, Tip. Preferred conservative substitutions includeGly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; andPhe, Tyr.

A “variant” of Orm2p typically has at least 25%, at least 50%, at least60% or at least 70%, preferably at least 80%, more preferably at least90%, even more preferably at least 95%, yet more preferably at least99%, most preferably at least 99.5% sequence identity to the sequence ofnative Orm2p.

The percent sequence identity between two polypeptides may be determinedusing suitable computer programs, as discussed below. Such variants may,or may not, be natural or made using the methods of protein engineeringand site-directed mutagenesis as are well known in the art.

A “fragment”, in the context of Orm2p, refers to a protein having thesequence of native Orm2p other than for at one or more positions wherethere have been deletions. Thus the fragment may, or may not, compriseat most 5, 10, 20, 30, 40 or 50%, typically up to 60%, more typically upto 70%, preferably up to 80%, more preferably up to 90%, even morepreferably up to 95%, yet more preferably up to 99% of the completesequence of the full mature Orm2p protein. Particularly preferredfragments of Orm2p protein comprise one or more whole domains of thedesired protein.

A fragment or variant of Orm2p may, or may not, be a protein that, whenexpressed recombinantly in a host cell, such as S. cerevisiae, cancomplement the deletion of the endogenous ORM2 gene in the host cell andmay, or may not, for example, be a naturally occurring homolog of Orm2p,such as a homolog encoded by another organism, such as another yeast orother fungi, or another eucaryote such as a human or other vertebrate,or animal or by a plant.

A gene encoding a protein comprising the sequence of a chaperone may, ormay not, be formed in a like manner to that discussed below for genesencoding heterologous proteins, with particular emphasis on combinationsof ORFs and regulatory regions.

Thus, one preferred chaperone is protein disulphide isomerase; anotherpreferred chaperone is Orm2p or a fragment or variant thereof. In aparticularly preferred embodiment, the first and second chaperones areprotein disulphide isomerase and Orm2p or a fragment or variant thereof.

Further preferred combinations for the first and second chaperones,respectively, may, or may not, be encoded by the genes AHA1 and CCT2;AHA1 and CCT3; AHA1 and CCT4; AHA1 and CCT5; AHA1 and CCT6; AHA1 andCCT7; AHA1 and CCT8; AHA1 and CNS1; AHA1 and CPR3; AHA1 and CPR6; AHA1and ERO1; AHA1 and EUG1; AHA1 and FMO1; AHA1 and HCH1; AHA1 and HSP10;AHA1 and HSP12; AHA1 and HSP104; AHA1 and HSP26; AHA1 and HSP30; AHA1and HSP42; AHA1 and HSP60; AHA1 and HSP78; AHA1 and HSP82; AHA1 andJEM1; AHA1 and MDJ1; AHA1 and MDJ2; AHA1 and MPD1; AHA1 and MPD2; AHA1and PDI1; AHA1 and PFD1; AHA1 and ABC1; AHA1 and APJ1; AHA1 and ATP11;AHA1 and ATP12; AHA1 and BTT1; AHA1 and CDC37; AHA1 and CPR7; AHA1 andHSC82; AHA1 and KAR2; AHA1 and LHS1; AHA1 and MGE1; AHA1 and MRS11; AHA1and NOB1; AHA1 and ECM10; AHA1 and SSA1; AHA1 and SSA2; AHA1 and SSA3;AHA1 and SSA4; AHA1 and SSC1; AHA1 and SSE2; AHA1 and SIL1; AHA1 andSLS1; AHA1 and ORM1; AHA1 and ORM2; AHA1 and PER1; AHA1 and PTC2; AHA1and PSE1; AHA1 and UBI4; AHA1 and HAC1 or a truncated intronless HAC1;CCT2 and CCT3; CCT2 and CCT4; CCT2 and CCT5; CCT2 and CCT6; CCT2 andCCT7; CCT2 and CCT8; CCT2 and CNS1; CCT2 and CPR3; CCT2 and CPR6; CCT2and ERO1; CCT2 and EUG1; CCT2 and FMO1; CCT2 and HCH1; CCT2 and HSP10;CCT2 and HSP12; CCT2 and HSP104; CCT2 and HSP26; CCT2 and HSP30; CCT2and HSP42; CCT2 and HSP60; CCT2 and HSP78; CCT2 and HSP82; CCT2 andJEM1; CCT2 and MDJ1; CCT2 and MDJ2; CCT2 and MPD1; CCT2 and MPD2; CCT2and PDI1; CCT2 and PFD1; CCT2 and ABC1; CCT2 and APJ1; CCT2 and ATP11;CCT2 and ATP12; CCT2 and BTT1; CCT2 and CDC37; CCT2 and CPR7; CCT2 andHSC82; CCT2 and KAR2; CCT2 and LHS1; CCT2 and MGE1; CCT2 and MRS11; CCT2and NOB1; CCT2 and ECM10; CCT2 and SSA1; CCT2 and SSA2; CCT2 and SSA3;CCT2 and SSA4; CCT2 and SSC1; CCT2 and SSE2; CCT2 and SIL1; CCT2 andSLS1; CCT2 and ORM1; CCT2 and ORM2; CCT2 and PER1; CCT2 and PTC2; CCT2and PSE1; CCT2 and UBI4; CCT2 and HAC1 or a truncated intronless HAC1;CCT3 and CCT4; CCT3 and CCT5; CCT3 and CCT6; CCT3 and CCT7; CCT3 andCCT8; CCT3 and CNS1; CCT3 and CPR3; CCT3 and CPR6; CCT3 and ERO1; CCT3and EUG1; CCT3 and FMO1; CCT3 and HCH1; CCT3 and HSP10; CCT3 and HSP12;CCT3 and HSP104; CCT3 and HSP26; CCT3 and HSP30; CCT3 and HSP42; CCT3and HSP60; CCT3 and HSP78; CCT3 and HSP82; CCT3 and JEM1; CCT3 and MDJ1;CCT3 and MDJ2; CCT3 and MPD1; CCT3 and MPD2; CCT3 and PDI1; CCT3 andPFD1; CCT3 and ABC1; CCT3 and APJ1; CCT3 and ATP11; CCT3 and ATP12; CCT3and BTT1; CCT3 and CDC37; CCT3 and CPR7; CCT3 and HSC82; CCT3 and KAR2;CCT3 and LHS1; CCT3 and MGE1; CCT3 and MRS11; CCT3 and NOB1; CCT3 andECM10; CCT3 and SSA1; CCT3 and SSA2; CCT3 and SSA3; CCT3 and SSA4; CCT3and SSC1; CCT3 and SSE2; CCT3 and SIL1; CCT3 and SLS1; CCT3 and ORM1;CCT3 and ORM2; CCT3 and PER1; CCT3 and PTC2; CCT3 and PSE1; CCT3 andUBI4; CCT3 and HAC1 or a truncated intronless HAC1; CCT4 and CCT5; CCT4and CCT6; CCT4 and CCT7; CCT4 and CCT8; CCT4 and CNS1; CCT4 and CPR3;CCT4 and CPR6; CCT4 and ERO1; CCT4 and EUG1; CCT4 and FMO1; CCT4 andHCH1; CCT4 and HSP10; CCT4 and HSP12; CCT4 and HSP104; CCT4 and HSP26;CCT4 and HSP30; CCT4 and HSP42; CCT4 and HSP60; CCT4 and HSP78; CCT4 andHSP82; CCT4 and JEM1; CCT4 and MDJ1; CCT4 and MDJ2; CCT4 and MPD1; CCT4and MPD2; CCT4 and PDI1; CCT4 and PFD1; CCT4 and ABC1; CCT4 and APJ1;CCT4 and ATP11; CCT4 and ATP12; CCT4 and BTT1; CCT4 and CDC37; CCT4 andCPR7; CCT4 and HSC82; CCT4 and KAR2; CCT4 and LHS1; CCT4 and MGE1; CCT4and MRS11; CCT4 and NOB1; CCT4 and ECM10; CCT4 and SSA1; CCT4 and SSA2;CCT4 and SSA3; CCT4 and SSA4; CCT4 and SSC1; CCT4 and SSE2; CCT4 andSIL1; CCT4 and SLS1; CCT4 and ORM1; CCT4 and ORM2; CCT4 and PER1; CCT4and PTC2; CCT4 and PSE1; CCT4 and UBI4; CCT4 and HAC1 or a truncatedintronless HAC1; CCT5 and CCT6; CCT5 and CCT7; CCT5 and CCT8; CCT5 andCNS1; CCT5 and CPR3; CCT5 and CPR6; CCT5 and ERO1; CCT5 and EUG1; CCT5and FMO1; CCT5 and HCH1; CCT5 and HSP10; CCT5 and HSP12; CCT5 andHSP104; CCT5 and HSP26; CCT5 and HSP30; CCT5 and HSP42; CCT5 and HSP60;CCT5 and HSP78; CCT5 and HSP82; CCT5 and JEM1; CCT5 and MDJ1; CCT5 andMDJ2; CCT5 and MPD1; CCT5 and MPD2; CCT5 and PDI1; CCT5 and PFD1; CCT5and ABC1; CCT5 and APJ1; CCT5 and ATP11; CCT5 and ATP12; CCT5 and BTT1;CCT5 and CDC37; CCT5 and CPR7; CCT5 and HSC82; CCT5 and KAR2; CCT5 andLHS1; CCT5 and MGE1; CCT5 and MRS11; CCT5 and NOB1; CCT5 and ECM10; CCT5and SSA1; CCT5 and SSA2; CCT5 and SSA3; CCT5 and SSA4; CCT5 and SSC1;CCT5 and SSE2; CCT5 and SIL1; CCT5 and SLS1; CCT5 and ORM1; CCT5 andORM2; CCT5 and PER1; CCT5 and PTC2; CCT5 and PSE1; CCT5 and UBI4; CCT5and HAC1 or a truncated intronless HAC1; CCT6 and CCT7; CCT6 and CCT8;CCT6 and CNS1; CCT6 and CPR3; CCT6 and CPR6; CCT6 and ERO1; CCT6 andEUG1; CCT6 and FMO1; CCT6 and HCH1; CCT6 and HSP10; CCT6 and HSP12; CCT6and HSP104; CCT6 and HSP26; CCT6 and HSP30; CCT6 and HSP42; CCT6 andHSP60; CCT6 and HSP78; CCT6 and HSP82; CCT6 and JEM1; CCT6 and MDJ1;CCT6 and MDJ2; CCT6 and MPD1; CCT6 and MPD2; CCT6 and PDI1; CCT6 andPFD1; CCT6 and ABC1; CCT6 and APJ1; CCT6 and ATP11; CCT6 and ATP12; CCT6and BTT1; CCT6 and CDC37; CCT6 and CPR7; CCT6 and HSC82; CCT6 and KAR2;CCT6 and LHS1; CCT6 and MGE1; CCT6 and MRS11; CCT6 and NOB1; CCT6 andECM10; CCT6 and SSA1; CCT6 and SSA2; CCT6 and SSA3; CCT6 and SSA4; CCT6and SSC1; CCT6 and SSE2; CCT6 and SIL1; CCT6 and SLS1; CCT6 and ORM1;CCT6 and ORM2; CCT6 and PER1; CCT6 and PTC2; CCT6 and PSE1; CCT6 andUBI4; CCT6 and HAC1 or a truncated intronless HAC1; CCT7 and CCT8; CCT7and CNS1; CCT7 and CPR3; CCT7 and CPR6; CCT7 and ERO1; CCT7 and EUG1;CCT7 and FMO1; CCT7 and HCH1; CCT7 and HSP10; CCT7 and HSP12; CCT7 andHSP104; CCT7 and HSP26; CCT7 and HSP30; CCT7 and HSP42; CCT7 and HSP60;CCT7 and HSP78; CCT7 and HSP82; CCT7 and JEM1; CCT7 and MDJ1; CCT7 andMDJ2; CCT7 and MPD1; CCT7 and MPD2; CCT7 and PDI1; CCT7 and PFD1; CCT7and ABC1; CCT7 and APJ1; CCT7 and ATP11; CCT7 and ATP12; CCT7 and BTT1;CCT7 and CDC37; CCT7 and CPR7; CCT7 and HSC82; CCT7 and KAR2; CCT7 andLHS1; CCT7 and MGE1; CCT7 and MRS11; CCT7 and NOB1; CCT7 and ECM10; CCT7and SSA1; CCT7 and SSA2; CCT7 and SSA3; CCT7 and SSA4; CCT7 and SSC1;CCT7 and SSE2; CCT7 and SIL1; CCT7 and SLS1; CCT7 and ORM1; CCT7 andORM2; CCT7 and PER1; CCT7 and PTC2; CCT7 and PSE1; CCT7 and UBI4; CCT7and HAC1 or a truncated intronless HAC1; CCT8 and CNS1; CCT8 and CPR3;CCT8 and CPR6; CCT8 and ERO1; CCT8 and EUG1; CCT8 and FMO1; CCT8 andHCH1; CCT8 and HSP10; CCT8 and HSP12; CCT8 and HSP104; CCT8 and HSP26;CCT8 and HSP30; CCT8 and HSP42; CCT8 and HSP60; CCT8 and HSP78; CCT8 andHSP82; CCT8 and JEM1; CCT8 and MDJ1; CCT8 and MDJ2; CCT8 and MPD1; CCT8and MPD2; CCT8 and PDI1; CCT8 and PFD1; CCT8 and ABC1; CCT8 and APJ1;CCT8 and ATP11; CCT8 and ATP12; CCT8 and BTT1; CCT8 and CDC37; CCT8 andCPR7; CCT8 and HSC82; CCT8 and KAR2; CCT8 and LHS1; CCT8 and MGE1; CCT8and MRS11; CCT8 and NOB1; CCT8 and ECM10; CCT8 and SSA1; CCT8 and SSA2;CCT8 and SSA3; CCT8 and SSA4; CCT8 and SSC1; CCT8 and SSE2; CCT8 andSIL1; CCT8 and SLS1; CCT8 and ORM1; CCT8 and ORM2; CCT8 and PER1; CCT8and PTC2; CCT8 and PSE1; CCT8 and UBI4; CCT8 and HAC1 or a truncatedintronless HAC1; CNS1 and CPR3; CNS1 and CPR6; CNS1 and ERO1; CNS1 andEUG1; CNS1 and FMO1; CNS1 and HCH1; CNS1 and HSP10; CNS1 and HSP12; CNS1and HSP104; CNS1 and HSP26; CNS1 and HSP30; CNS1 and HSP42; CNS1 andHSP60; CNS1 and HSP78; CNS1 and HSP82; CNS1 and JEM1; CNS1 and MDJ1;CNS1 and MDJ2; CNS1 and MPD1; CNS1 and MPD2; CNS1 and PDI1; CNS1 andPFD1; CNS1 and ABC1; CNS1 and APJ1; CNS1 and ATP11; CNS1 and ATP12; CNS1and BTT1; CNS1 and CDC37; CNS1 and CPR7; CNS1 and HSC82; CNS1 and KAR2;CNS1 and LHS1; CNS1 and MGE1; CNS1 and MRS11; CNS1 and NOB1; CNS1 andECM10; CNS1 and SSA1; CNS1 and SSA2; CNS1 and SSA3; CNS1 and SSA4; CNS1and SSC1; CNS1 and SSE2; CNS1 and SIL1; CNS1 and SLS1; CNS1 and ORM1;CNS1 and ORM2; CNS1 and PER1; CNS1 and PTC2; CNS1 and PSE1; CNS1 andUBI4; CNS1 and HAC1 or a truncated intronless HAC1; CPR3 and CPR6; CPR3and ERO1; CPR3 and EUG1; CPR3 and FMO1; CPR3 and HCH1; CPR3 and HSP10;CPR3 and HSP12; CPR3 and HSP104; CPR3 and HSP26; CPR3 and HSP30; CPR3and HSP42; CPR3 and HSP60; CPR3 and HSP78; CPR3 and HSP82; CPR3 andJEM1; CPR3 and MDJ1; CPR3 and MDJ2; CPR3 and MPD1; CPR3 and MPD2; CPR3and PDI1; CPR3 and PFD1; CPR3 and ABC1; CPR3 and APJ1; CPR3 and ATP11;CPR3 and ATP12; CPR3 and BTT1; CPR3 and CDC37; CPR3 and CPR7; CPR3 andHSC82; CPR3 and KAR2; CPR3 and LHS1; CPR3 and MGE1; CPR3 and MRS11; CPR3and NOB1; CPR3 and ECM10; CPR3 and SSA1; CPR3 and SSA2; CPR3 and SSA3;CPR3 and SSA4; CPR3 and SSC1; CPR3 and SSE2; CPR3 and SIL1; CPR3 andSLS1; CPR3 and ORM1; CPR3 and ORM2; CPR3 and PER1; CPR3 and PTC2; CPR3and PSE1; CPR3 and UBI4; CPR3 and HAC1 or a truncated intronless HAC1;CPR6 and ERO1; CPR6 and EUG1; CPR6 and FMO1; CPR6 and HCH1; CPR6 andHSP10; CPR6 and HSP12; CPR6 and HSP104; CPR6 and HSP26; CPR6 and HSP30;CPR6 and HSP42; CPR6 and HSP60; CPR6 and HSP78; CPR6 and HSP82; CPR6 andJEM1; CPR6 and MDJ1; CPR6 and MDJ2; CPR6 and MPD1; CPR6 and MPD2; CPR6and PDI1; CPR6 and PFD1; CPR6 and ABC1; CPR6 and APJ1; CPR6 and ATP11;CPR6 and ATP12; CPR6 and BTT1; CPR6 and CDC37; CPR6 and CPR7; CPR6 andHSC82; CPR6 and KAR2; CPR6 and LHS1; CPR6 and MGE1; CPR6 and MRS11; CPR6and NOB1; CPR6 and ECM10; CPR6 and SSA1; CPR6 and SSA2; CPR6 and SSA3;CPR6 and SSA4; CPR6 and SSC1; CPR6 and SSE2; CPR6 and SIL1; CPR6 andSLS1; CPR6 and ORM1; CPR6 and ORM2; CPR6 and PER1; CPR6 and PTC2; CPR6and PSE1; CPR6 and UBI4; CPR6 and HAC1 or a truncated intronless HAC1;ERO1 and EUG1; ERO1 and FMO1; ERO1 and HCH1; ERO1 and HSP10; ERO1 andHSP12; ERO1 and HSP104; ERO1 and HSP26; ERO1 and HSP30; ERO1 and HSP42;ERO1 and HSP60; ERO1 and HSP78; ERO1 and HSP82; ERO1 and JEM1; ERO1 andMDJ1; ERO1 and MDJ2; ERO1 and MPD1; ERO1 and MPD2; ERO1 and PDI1; ERO1and PFD1; ERO1 and ABC1; ERO1 and APJ1; ERO1 and ATP11; ERO1 and ATP12;ERO1 and BTT1; ERO1 and CDC37; ERO1 and CPR7; ERO1 and HSC82; ERO1 andKAR2; ERO1 and LHS1; ERO1 and MGE1; ERO1 and MRS11; ERO1 and NOB1; ERO1and ECM10; ERO1 and SSA1; ERO1 and SSA2; ERO1 and SSA3; ERO1 and SSA4;ERO1 and SSC1; ERO1 and SSE2; ERO1 and SIL1; ERO1 and SLS1; ERO1 andORM1; ERO1 and ORM2; ERO1 and PER1; ERO1 and PTC2; ERO1 and PSE1; ERO1and UBI4; ERO1 and HAC1 or a truncated intronless HAC1; EUG1 and FMO1;EUG1 and HCH1; EUG1 and HSP10; EUG1 and HSP12; EUG1 and HSP104; EUG1 andHSP26; EUG1 and HSP30; EUG1 and HSP42; EUG1 and HSP60; EUG1 and HSP78;EUG1 and HSP82; EUG1 and JEM1; EUG1 and MDJ1; EUG1 and MDJ2; EUG1 andMPD1; EUG1 and MPD2; EUG1 and PDI1; EUG1 and PFD1; EUG1 and ABC1; EUG1and APJ1; EUG1 and ATP11; EUG1 and ATP12; EUG1 and BTT1; EUG1 and CDC37;EUG1 and CPR7; EUG1 and HSC82; EUG1 and KAR2; EUG1 and LHS1; EUG1 andMGE1; EUG1 and MRS11; EUG1 and NOB1; EUG1 and ECM10; EUG1 and SSA1; EUG1and SSA2; EUG1 and SSA3; EUG1 and SSA4; EUG1 and SSC1; EUG1 and SSE2;EUG1 and SIL1; EUG1 and SLS1; EUG1 and ORM1; EUG1 and ORM2; EUG1 andPER1; EUG1 and PTC2; EUG1 and PSE1; EUG1 and UBI4; EUG1 and HAC1 or atruncated intronless HAC1; FMO1 and HCH1; FMO1 and HSP10; FMO1 andHSP12; FMO1 and HSP104; FMO1 and HSP26; FMO1 and HSP30; FMO1 and HSP42;FMO1 and HSP60; FMO1 and HSP78; FMO1 and HSP82; FMO1 and JEM1; FMO1 andMDJ1; FMO1 and MDJ2; FMO1 and MPD1; FMO1 and MPD2; FMO1 and PDI1; FMO1and PFD1; FMO1 and ABC1; FMO1 and APJ1; FMO1 and ATP11; FMO1 and ATP12;FMO1 and BTT1; FMO1 and CDC37; FMO1 and CPR7; FMO1 and HSC82; FMO1 andKAR2; FMO1 and LHS1; FMO1 and MGE1; FMO1 and MRS11; FMO1 and NOB1; FMO1and ECM10; FMO1 and SSA1; FMO1 and SSA2; FMO1 and SSA3; FMO1 and SSA4;FMO1 and SSC1; FMO1 and SSE2; FMO1 and SIL1; FMO1 and SLS1; FMO1 andORM1; FMO1 and ORM2; FMO1 and PER1; FMO1 and PTC2; FMO1 and PSE1; FMO1and UBI4; FMO1 and HAC1 or a truncated intronless HAC1; HCH1 and HSP10;HCH1 and HSP12; HCH1 and HSP104; HCH1 and HSP26; HCH1 and HSP30; HCH1and HSP42; HCH1 and HSP60; HCH1 and HSP78; HCH1 and HSP82; HCH1 andJEM1; HCH1 and MDJ1; HCH1 and MDJ2; HCH1 and MPD1; HCH1 and MPD2; HCH1and PDI1; HCH1 and PFD1; HCH1 and ABC1; HCH1 and APJ1; HCH1 and ATP11;HCH1 and ATP12; HCH1 and BTT1; HCH1 and CDC37; HCH1 and CPR7; HCH1 andHSC82; HCH1 and KAR2; HCH1 and LHS1; HCH1 and MGE1; HCH1 and MRS11; HCH1and NOB1; HCH1 and ECM10; HCH1 and SSA1; HCH1 and SSA2; HCH1 and SSA3;HCH1 and SSA4; HCH1 and SSC1; HCH1 and SSE2; HCH1 and SIL1; HCH1 andSLS1; HCH1 and ORM1; HCH1 and ORM2; HCH1 and PER1; HCH1 and PTC2; HCH1and PSE1; HCH1 and UBI4; HCH1 and HAC1 or a truncated intronless HAC1;HSP10 and HSP12; HSP10 and HSP104; HSP10 and HSP26; HSP10 and HSP30;HSP10 and HSP42; HSP10 and HSP60; HSP10 and HSP78; HSP10 and HSP82;HSP10 and JEM1; HSP10 and MDJ1; HSP10 and MDJ2; HSP10 and MPD1; HSP10and MPD2; HSP10 and PDI1; HSP10 and PFD1; HSP10 and ABC1; HSP10 andAPJ1; HSP10 and ATP11; HSP10 and ATP12; HSP10 and BTT1; HSP10 and CDC37;HSP10 and CPR7; HSP10 and HSC82; HSP10 and KAR2; HSP10 and LHS1; HSP10and MGE1; HSP10 and MRS11; HSP10 and NOB1; HSP10 and ECM10; HSP10 andSSA1; HSP10 and SSA2; HSP10 and SSA3; HSP10 and SSA4; HSP10 and SSC1;HSP10 and SSE2; HSP10 and SIL1; HSP10 and SLS1; HSP10 and ORM1; HSP10and ORM2; HSP10 and PER1; HSP10 and PTC2; HSP10 and PSE1; HSP10 andUBI4; HSP10 and HAC1 or a truncated intronless HAC1; HSP12 and HSP104;HSP12 and HSP26; HSP12 and HSP30; HSP12 and HSP42; HSP12 and HSP60;HSP12 and HSP78; HSP12 and HSP82; HSP12 and JEM1; HSP12 and MDJ1; HSP12and MDJ2; HSP12 and MPD1; HSP12 and MPD2; HSP12 and PDI1; HSP12 andPFD1; HSP12 and ABC1; HSP12 and APJ1; HSP12 and ATP11; HSP12 and ATP12;HSP12 and BTT1; HSP12 and CDC37; HSP12 and CPR7; HSP12 and HSC82; HSP12and KAR2; HSP12 and LHS1; HSP12 and MGE1; HSP12 and MRS11; HSP12 andNOB1; HSP12 and ECM10; HSP12 and SSA1; HSP12 and SSA2; HSP12 and SSA3;HSP12 and SSA4; HSP12 and SSC1; HSP12 and SSE2; HSP12 and SIL1; HSP12and SLS1; HSP12 and ORM1; HSP12 and ORM2; HSP12 and PER1; HSP12 andPTC2; HSP12 and PSE1; HSP12 and UBI4; HSP12 and HAC1 or a truncatedintronless HAC1; HSP104 and HSP26; HSP104 and HSP30; HSP104 and HSP42;HSP104 and HSP60; HSP104 and HSP78; HSP104 and HSP82; HSP104 and JEM1;HSP104 and MDJ1; HSP104 and MDJ2; HSP104 and MPD1; HSP104 and MPD2;HSP104 and PDI1; HSP104 and PFD1; HSP104 and ABC1; HSP104 and APJ1;HSP104 and ATP11; HSP104 and ATP12; HSP104 and BTT1; HSP104 and CDC37;HSP104 and CPR7; HSP104 and HSC82; HSP104 and KAR2; HSP104 and LHS1;HSP104 and MGE1; HSP104 and MRS11; HSP104 and NOB1; HSP104 and ECM10;HSP104 and SSA1; HSP104 and SSA2; HSP104 and SSA3; HSP104 and SSA4;HSP104 and SSC1; HSP104 and SSE2; HSP104 and SIL1; HSP104 and SLS1;HSP104 and ORM1; HSP104 and ORM2; HSP104 and PER1; HSP104 and PTC2;HSP104 and PSE1; HSP104 and UBI4; HSP104 and HAC1 or a truncatedintronless HAC1; HSP26 and HSP30; HSP26 and HSP42; HSP26 and HSP60;HSP26 and HSP78; HSP26 and HSP82; HSP26 and JEM1; HSP26 and MDJ1; HSP26and MDJ2; HSP26 and MPD1; HSP26 and MPD2; HSP26 and PDI1; HSP26 andPFD1; HSP26 and ABC1; HSP26 and APJ1; HSP26 and ATP11; HSP26 and ATP12;HSP26 and BTT1; HSP26 and CDC37; HSP26 and CPR7; HSP26 and HSC82; HSP26and KAR2; HSP26 and LHS1; HSP26 and MGE1; HSP26 and MRS11; HSP26 andNOB1; HSP26 and ECM10; HSP26 and SSA1; HSP26 and SSA2; HSP26 and SSA3;HSP26 and SSA4; HSP26 and SSC1; HSP26 and SSE2; HSP26 and SIL1; HSP26and SLS1; HSP26 and ORM1; HSP26 and ORM2; HSP26 and PER1; HSP26 andPTC2; HSP26 and PSE1; HSP26 and UBI4; HSP26 and HAC1 or a truncatedintronless HAC1; HSP30 and HSP42; HSP30 and HSP60; HSP30 and HSP78;HSP30 and HSP82; HSP30 and JEM1; HSP30 and MDJ1; HSP30 and MDJ2; HSP30and MPD1; HSP30 and MPD2; HSP30 and PDI1; HSP30 and PFD1; HSP30 andABC1; HSP30 and APJ1; HSP30 and ATP11; HSP30 and ATP12; HSP30 and BTT1;HSP30 and CDC37; HSP30 and CPR7; HSP30 and HSC82; HSP30 and KAR2; HSP30and LHS1; HSP30 and MGE1; HSP30 and MRS11; HSP30 and NOB1; HSP30 andECM10; HSP30 and SSA1; HSP30 and SSA2; HSP30 and SSA3; HSP30 and SSA4;HSP30 and SSC1; HSP30 and SSE2; HSP30 and SIL1; HSP30 and SLS1; HSP30and ORM1; HSP30 and ORM2; HSP30 and PER1; HSP30 and PTC2; HSP30 andPSE1; HSP30 and UBI4; HSP30 and HAC1 or a truncated intronless HAC1;HSP42 and HSP60; HSP42 and HSP78; HSP42 and HSP82; HSP42 and JEM1; HSP42and MDJ1; HSP42 and MDJ2; HSP42 and MPD1; HSP42 and MPD2; HSP42 andPDI1; HSP42 and PFD1; HSP42 and ABC1; HSP42 and APJ1; HSP42 and ATP11;HSP42 and ATP12; HSP42 and BTT1; HSP42 and CDC37; HSP42 and CPR7; HSP42and HSC82; HSP42 and KAR2; HSP42 and LHS1; HSP42 and MGE1; HSP42 andMRS11; HSP42 and NOB1; HSP42 and ECM10; HSP42 and SSA1; HSP42 and SSA2;HSP42 and SSA3; HSP42 and SSA4; HSP42 and SSC1; HSP42 and SSE2; HSP42and SIL1; HSP42 and SLS1; HSP42 and ORM1; HSP42 and ORM2; HSP42 andPER1; HSP42 and PTC2; HSP42 and PSE1; HSP42 and UBI4; HSP42 and HAC1 ora truncated intronless HAC1; HSP60 and HSP78; HSP60 and HSP82; HSP60 andJEM1; HSP60 and MDJ1; HSP60 and MDJ2; HSP60 and MPD1; HSP60 and MPD2;HSP60 and PDI1; HSP60 and PFD1; HSP60 and ABC1; HSP60 and APJ1; HSP60and ATP11; HSP60 and ATP12; HSP60 and BTT1; HSP60 and CDC37; HSP60 andCPR7; HSP60 and HSC82; HSP60 and KAR2; HSP60 and LHS1; HSP60 and MGE1;HSP60 and MRS11; HSP60 and NOB1; HSP60 and ECM10; HSP60 and SSA1; HSP60and SSA2; HSP60 and SSA3; HSP60 and SSA4; HSP60 and SSC1; HSP60 andSSE2; HSP60 and SIL1; HSP60 and SLS1; HSP60 and ORM1; HSP60 and ORM2;HSP60 and PER1; HSP60 and PTC2; HSP60 and PSE1; HSP60 and UBI4; HSP60and HAC1 or a truncated intronless HAC1; HSP78 and HSP82; HSP78 andJEM1; HSP78 and MDJ1; HSP78 and MDJ2; HSP78 and MPD1; HSP78 and MPD2;HSP78 and PDI1; HSP78 and PFD1; HSP78 and ABC1; HSP78 and APJ1; HSP78and ATP11; HSP78 and ATP12; HSP78 and BTT1; HSP78 and CDC37; HSP78 andCPR7; HSP78 and HSC82; HSP78 and KAR2; HSP78 and LHS1; HSP78 and MGE1;HSP78 and MRS11; HSP78 and NOB1; HSP78 and ECM10; HSP78 and SSA1; HSP78and SSA2; HSP78 and SSA3; HSP78 and SSA4; HSP78 and SSC1; HSP78 andSSE2; HSP78 and SIL1; HSP78 and SLS1; HSP78 and ORM1; HSP78 and ORM2;HSP78 and PER1; HSP78 and PTC2; HSP78 and PSE1; HSP78 and UBI4; HSP78and HAC1 or a truncated intronless HAC1; HSP82 and JEM1; HSP82 and MDJ1;HSP82 and MDJ2; HSP82 and MPD1; HSP82 and MPD2; HSP82 and PDI1; HSP82and PFD1; HSP82 and ABC1; HSP82 and APJ1; HSP82 and ATP11; HSP82 andATP12; HSP82 and BTT1; HSP82 and CDC37; HSP82 and CPR7; HSP82 and HSC82;HSP82 and KAR2; HSP82 and LHS1; HSP82 and MGE1; HSP82 and MRS11; HSP82and NOB1; HSP82 and ECM10; HSP82 and SSA1; HSP82 and SSA2; HSP82 andSSA3; HSP82 and SSA4; HSP82 and SSC1; HSP82 and SSE2; HSP82 and SIL1;HSP82 and SLS1; HSP82 and ORM1; HSP82 and ORM2; HSP82 and PER1; HSP82and PTC2; HSP82 and PSE1; HSP82 and UBI4; HSP82 and HAC1 or a truncatedintronless HAC1; JEM1 and MDJ1; JEM1 and MDJ2; JEM1 and MPD1; JEM1 andMPD2; JEM1 and PDI1; JEM1 and PFD1; JEM1 and ABC1; JEM1 and APJ1; JEM1and ATP11; JEM1 and ATP12; JEM1 and BTT1; JEM1 and CDC37; JEM1 and CPR7;JEM1 and HSC82; JEM1 and KAR2; JEM1 and LHS1; JEM1 and MGE1; JEM1 andMRS11; JEM1 and NOB1; JEM1 and ECM10; JEM1 and SSA1; JEM1 and SSA2; JEM1and SSA3; JEM1 and SSA4; JEM1 and SSC1; JEM1 and SSE2; JEM1 and SIL1;JEM1 and SLS1; JEM1 and ORM1; JEM1 and ORM2; JEM1 and PER1; JEM1 andPTC2; JEM1 and PSE1; JEM1 and UBI4; JEM1 and HAC1 or a truncatedintronless HAC1; MDJ1 and MDJ2; MDJ1 and MPD1; MDJ1 and MPD2; MDJ1 andPDI1; MDJ1 and PFD1; MDJ1 and ABC1; MDJ1 and APJ1; MDJ1 and ATP11; MDJ1and ATP12; MDJ1 and BTT1; MDJ1 and CDC37; MDJ1 and CPR7; MDJ1 and HSC82;MDJ1 and KAR2; MDJ1 and LHS1; MDJ1 and MGE1; MDJ1 and MRS11; MDJ1 andNOB1; MDJ1 and ECM10; MDJ1 and SSA1; MDJ1 and SSA2; MDJ1 and SSA3; MDJ1and SSA4; MDJ1 and SSC1; MDJ1 and SSE2; MDJ1 and SIL1; MDJ1 and SLS1;MDJ1 and ORM1; MDJ1 and ORM2; MDJ1 and PER1; MDJ1 and PTC2; MDJ1 andPSE1; MDJ1 and UBI4; MDJ1 and HAC1 or a truncated intronless HAC1; MDJ2and MPD1; MDJ2 and MPD2; MDJ2 and PDI1; MDJ2 and PFD1; MDJ2 and ABC1;MDJ2 and APJ1; MDJ2 and ATP11; MDJ2 and ATP12; MDJ2 and BTT1; MDJ2 andCDC37; MDJ2 and CPR7; MDJ2 and HSC82; MDJ2 and KAR2; MDJ2 and LHS1; MDJ2and MGE1; MDJ2 and MRS11; MDJ2 and NOB1; MDJ2 and ECM10; MDJ2 and SSA1;MDJ2 and SSA2; MDJ2 and SSA3; MDJ2 and SSA4; MDJ2 and SSC1; MDJ2 andSSE2; MDJ2 and SIL1; MDJ2 and SLS1; MDJ2 and ORM1; MDJ2 and ORM2; MDJ2and PER1; MDJ2 and PTC2; MDJ2 and PSE1; MDJ2 and UBI4; MDJ2 and HAC1 ora truncated intronless HAC1; MPD1 and MPD2; MPD1 and PDI1; MPD1 andPFD1; MPD1 and ABC1; MPD1 and APJ1; MPD1 and ATP11; MPD1 and ATP12; MPD1and BTT1; MPD1 and CDC37; MPD1 and CPR7; MPD1 and HSC82; MPD1 and KAR2;MPD1 and LHS1; MPD1 and MGE1; MPD1 and MRS11; MPD1 and NOB1; MPD1 andECM10; MPD1 and SSA1; MPD1 and SSA2; MPD1 and SSA3; MPD1 and SSA4; MPD1and SSC1; MPD1 and SSE2; MPD1 and SIL1; MPD1 and SLS1; MPD1 and ORM1;MPD1 and ORM2; MPD1 and PER1; MPD1 and PTC2; MPD1 and PSE1; MPD1 andUBI4; MPD1 and HAC1 or a truncated intronless HAC1; MPD2 and PDI1; MPD2and PFD1; MPD2 and ABC1; MPD2 and APJ1; MPD2 and ATP11; MPD2 and ATP12;MPD2 and BTT1; MPD2 and CDC37; MPD2 and CPR7; MPD2 and HSC82; MPD2 andKAR2; MPD2 and LHS1; MPD2 and MGE1; MPD2 and MRS11; MPD2 and NOB1; MPD2and ECM10; MPD2 and SSA1; MPD2 and SSA2; MPD2 and SSA3; MPD2 and SSA4;MPD2 and SSC1; MPD2 and SSE2; MPD2 and SIL1; MPD2 and SLS1; MPD2 andORM1; MPD2 and ORM2; MPD2 and PER1; MPD2 and PTC2; MPD2 and PSE1; MPD2and UBI4; MPD2 and HAC1 or a truncated intronless HAC1; PDI1 and PFD1;PDI1 and ABC1; PDI1 and APJ1; PDI1 and ATP11; PDI1 and ATP12; PDI1 andBTT1; PDI1 and CDC37; PDI1 and CPR7; PDI1 and HSC82; PDI1 and KAR2; PDI1and LHS1; PDI1 and MGE1; PDI1 and MRS11; PDI1 and NOB1; PDI1 and ECM10;PDI1 and SSA1; PDI1 and SSA2; PDI1 and SSA3; PDI1 and SSA4; PDI1 andSSC1; PDI1 and SSE2; PDI1 and SIL1; PDI1 and SLS1; PDI1 and ORM1; PDI1and ORM2; PDI1 and PER1; PDI1 and PTC2; PDI1 and PSE1; PDI1 and UBI4;PDI1 and HAC1 or a truncated intronless HAC1; PFD1 and ABC1; PFD1 andAPJ1; PFD1 and ATP11; PFD1 and ATP12; PFD1 and BTT1; PFD1 and CDC37;PFD1 and CPR7; PFD1 and HSC82; PFD1 and KAR2; PFD1 and LHS1; PFD1 andMGE1; PFD1 and MRS11; PFD1 and NOB1; PFD1 and ECM10; PFD1 and SSA1; PFD1and SSA2; PFD1 and SSA3; PFD1 and SSA4; PFD1 and SSC1; PFD1 and SSE2;PFD1 and SIL1; PFD1 and SLS1; PFD1 and ORM1; PFD1 and ORM2; PFD1 andPER1; PFD1 and PTC2; PFD1 and PSE1; PFD1 and UBI4; PFD1 and HAC1 or atruncated intronless HAC1; ABC1 and APJ1; ABC1 and ATP11; ABC1 andATP12; ABC1 and BTT1; ABC1 and CDC37; ABC1 and CPR7; ABC1 and HSC82;ABC1 and KAR2; ABC1 and LHS1; ABC1 and MGE1; ABC1 and MRS11; ABC1 andNOB1; ABC1 and ECM10; ABC1 and SSA1; ABC1 and SSA2; ABC1 and SSA3; ABC1and SSA4; ABC1 and SSC1; ABC1 and SSE2; ABC1 and SIL1; ABC1 and SLS1;ABC1 and ORM1; ABC1 and ORM2; ABC1 and PER1; ABC1 and PTC2; ABC1 andPSE1; ABC1 and UBI4; ABC1 and HAC1 or a truncated intronless HAC1; APJ1and ATP11; APJ1 and ATP12; APJ1 and BTT1; APJ1 and CDC37; APJ1 and CPR7;APJ1 and HSC82; APJ1 and KAR2; APJ1 and LHS1; APJ1 and MGE1; APJ1 andMRS11; APJ1 and NOB1; APJ1 and ECM10; APJ1 and SSA1; APJ1 and SSA2; APJ1and SSA3; APJ1 and SSA4; APJ1 and SSC1; APJ1 and SSE2; APJ1 and SIL1;APJ1 and SLS1; APJ1 and ORM1; APJ1 and ORM2; APJ1 and PER1; APJ1 andPTC2; APJ1 and PSE1; APJ1 and UBI4; APJ1 and HAC1 or a truncatedintronless HAC1; ATP11 and ATP12; ATP11 and BTT1; ATP11 and CDC37; ATP11and CPR7; ATP11 and HSC82; ATP11 and KAR2; ATP11 and LHS1; ATP11 andMGE1; ATP11 and MRS11; ATP11 and NOB1; ATP11 and ECM10; ATP11 and SSA1;ATP11 and SSA2; ATP11 and SSA3; ATP11 and SSA4; ATP11 and SSC1; ATP11and SSE2; ATP11 and SIL1; ATP11 and SLS1; ATP11 and ORM1; ATP11 andORM2; ATP11 and PER1; ATP11 and PTC2; ATP11 and PSE1; ATP11 and UBI4;ATP11 and HAC1 or a truncated intronless HAC1; ATP12 and BTT1; ATP12 andCDC37; ATP12 and CPR7; ATP12 and HSC82; ATP12 and KAR2; ATP12 and LHS1;ATP12 and MGE1; ATP12 and MRS11; ATP12 and NOB1; ATP12 and ECM10; ATP12and SSA1; ATP12 and SSA2; ATP12 and SSA3; ATP12 and SSA4; ATP12 andSSC1; ATP12 and SSE2; ATP12 and SIL1; ATP12 and SLS1; ATP12 and ORM1;ATP12 and ORM2; ATP12 and PER1; ATP12 and PTC2; ATP12 and PSE1; ATP12and UBI4; ATP12 and HAC1 or a truncated intronless HAC1; BTT1 and CDC37;BTT1 and CPR7; BTT1 and HSC82; BTT1 and KAR2; BTT1 and LHS1; BTT1 andMGE1; BTT1 and MRS11; BTT1 and NOB1; BTT1 and ECM10; BTT1 and SSA1; BTT1and SSA2; BTT1 and SSA3; BTT1 and SSA4; BTT1 and SSC1; BTT1 and SSE2;BTT1 and SIL1; BTT1 and SLS1; BTT1 and ORM1; BTT1 and ORM2; BTT1 andPER1; BTT1 and PTC2; BTT1 and PSE1; BTT1 and UBI4; BTT1 and HAC1 or atruncated intronless HAC1; CDC37 and CPR7; CDC37 and HSC82; CDC37 andKAR2; CDC37 and LHS1; CDC37 and MGE1; CDC37 and MRS11; CDC37 and NOB1;CDC37 and ECM10; CDC37 and SSA1; CDC37 and SSA2; CDC37 and SSA3; CDC37and SSA4; CDC37 and SSC1; CDC37 and SSE2; CDC37 and SIL1; CDC37 andSLS1; CDC37 and ORM1; CDC37 and ORM2; CDC37 and PER1; CDC37 and PTC2;CDC37 and PSE1; CDC37 and UBI4; CDC37 and HAC1 or a truncated intronlessHAC1; CPR7 and HSC82; CPR7 and KAR2; CPR7 and LHS1; CPR7 and MGE1; CPR7and MRS11; CPR7 and NOB1; CPR7 and ECM10; CPR7 and SSA1; CPR7 and SSA2;CPR7 and SSA3; CPR7 and SSA4; CPR7 and SSC1; CPR7 and SSE2; CPR7 andSIL1; CPR7 and SLS1; CPR7 and ORM1; CPR7 and ORM2; CPR7 and PER1; CPR7and PTC2; CPR7 and PSE1; CPR7 and UBI4; CPR7 and HAC1 or a truncatedintronless HAC1; HSC82 and KAR2; HSC82 and LHS1; HSC82 and MGE1; HSC82and MRS11; HSC82 and NOB1; HSC82 and ECM10; HSC82 and SSA1; HSC82 andSSA2; HSC82 and SSA3; HSC82 and SSA4; HSC82 and SSC1; HSC82 and SSE2;HSC82 and SIL1; HSC82 and SLS1; HSC82 and ORM1; HSC82 and ORM2; HSC82and PER1; HSC82 and PTC2; HSC82 and PSE1; HSC82 and UBI4; HSC82 and HAC1or a truncated intronless HAC1; KAR2 and LHS1; KAR2 and MGE1; KAR2 andMRS11; KAR2 and NOB1; KAR2 and ECM10; KAR2 and SSA1; KAR2 and SSA2; KAR2and SSA3; KAR2 and SSA4; KAR2 and SSC1; KAR2 and SSE2; KAR2 and SIL1;KAR2 and SLS1; KAR2 and ORM1; KAR2 and ORM2; KAR2 and PER1; KAR2 andPTC2; KAR2 and PSE1; KAR2 and UBI4; KAR2 and HAC1 or a truncatedintronless HAC1; LHS1 and MGE1; LHS1 and MRS11; LHS1 and NOB1; LHS1 andECM10; LHS1 and SSA1; LHS1 and SSA2; LHS1 and SSA3; LHS1 and SSA4; LHS1and SSC1; LHS1 and SSE2; LHS1 and SIL1; LHS1 and SLS1; LHS1 and ORM1;LHS1 and ORM2; LHS1 and PER1; LHS1 and PTC2; LHS1 and PSE1; LHS1 andUBI4; LHS1 and HAC1 or a truncated intronless HAC1; MGE1 and MRS11; MGE1and NOB1; MGE1 and ECM10; MGE1 and SSA1; MGE1 and SSA2; MGE1 and SSA3;MGE1 and SSA4; MGE1 and SSC1; MGE1 and SSE2; MGE1 and SIL1; MGE1 andSLS1; MGE1 and ORM1; MGE1 and ORM2; MGE1 and PER1; MGE1 and PTC2; MGE1and PSE1; MGE1 and UBI4; MGE1 and HAC1 or a truncated intronless HAC1;MRS11 and NOB1; MRS11 and ECM10; MRS11 and SSA1; MRS11 and SSA2; MRS11and SSA3; MRS11 and SSA4; MRS11 and SSC1; MRS11 and SSE2; MRS11 andSIL1; MRS11 and SLS1; MRS11 and ORM1; MRS11 and ORM2; MRS11 and PER1;MRS11 and PTC2; MRS11 and PSE1; MRS11 and UBI4; MRS11 and HAC1 or atruncated intronless HAC1; NOB1 and ECM10; NOB1 and SSA1; NOB1 and SSA2;NOB1 and SSA3; NOB1 and SSA4; NOB1 and SSC1; NOB1 and SSE2; NOB1 andSIL1; NOB1 and SLS1; NOB1 and ORM1; NOB1 and ORM2; NOB1 and PER1; NOB1and PTC2; NOB1 and PSE1; NOB1 and UBI4; NOB1 and HAC1 or a truncatedintronless HAC1; ECM10 and SSA1; ECM10 and SSA2; ECM10 and SSA3; ECM10and SSA4; ECM10 and SSC1; ECM10 and SSE2; ECM10 and SIL1; ECM10 andSLS1; ECM10 and ORM1; ECM10 and ORM2; ECM10 and PER1; ECM10 and PTC2;ECM10 and PSE1; ECM10 and UBI4; ECM10 and HAC1 or a truncated intronlessHAC1; SSA1 and SSA2; SSA1 and SSA3; SSA1 and SSA4; SSA1 and SSC1; SSA1and SSE2; SSA1 and SIL1; SSA1 and SLS1; SSA1 and ORM1; SSA1 and ORM2;SSA1 and PER1; SSA1 and PTC2; SSA1 and PSE1; SSA1 and UBI4; SSA1 andHAC1 or a truncated intronless HAC1; SSA2 and SSA3; SSA2 and SSA4; SSA2and SSC1; SSA2 and SSE2; SSA2 and SIL1; SSA2 and SLS1; SSA2 and ORM1;SSA2 and ORM2; SSA2 and PER1; SSA2 and PTC2; SSA2 and PSE1; SSA2 andUBI4; SSA2 and HAC1 or a truncated intronless HAC1; SSA3 and SSA4; SSA3and SSC1; SSA3 and SSE2; SSA3 and SIL1; SSA3 and SLS1; SSA3 and ORM1;SSA3 and ORM2; SSA3 and PER1; SSA3 and PTC2; SSA3 and PSE1; SSA3 andUBI4; SSA3 and HAC1 or a truncated intronless HAC1; SSA4 and SSC1; SSA4and SSE2; SSA4 and SIL1; SSA4 and SLS1; SSA4 and ORM1; SSA4 and ORM2;SSA4 and PER1; SSA4 and PTC2; SSA4 and PSE1; SSA4 and UBI4; SSA4 andHAC1 or a truncated intronless HAC1; SSC1 and SSE2; SSC1 and SIL1; SSC1and SLS1; SSC1 and ORM1; SSC1 and ORM2; SSC1 and PER1; SSC1 and PTC2;SSC1 and PSE1; SSC1 and UBI4; SSC1 and HAC1 or a truncated intronlessHAC1; SSE2 and SIL1; SSE2 and SLS1; SSE2 and ORM1; SSE2 and ORM2; SSE2and PER1; SSE2 and PTC2; SSE2 and PSE1; SSE2 and UBI4; SSE2 and HAC1 ora truncated intronless HAC1; SIL1 and SLS1; SIL1 and ORM1; SIL1 andORM2; SIL1 and PER1; SIL1 and PTC2; SIL1 and PSE1; SIL1 and UBI4; SIL1and HAC1 or a truncated intronless HAC1; SLS1 and ORM1; SLS1 and ORM2;SLS1 and PER1; SLS1 and PTC2; SLS1 and PSE1; SLS1 and UBI4; SLS1 andHAC1 or a truncated intronless HAC1; ORM1 and ORM2; ORM1 and PER1; ORM1and PTC2; ORM1 and PSE1; ORM1 and UBI4; ORM1 and HAC1 or a truncatedintronless HAC1; ORM2 and PER1; ORM2 and PTC2; ORM2 and PSE1; ORM2 andUBI4; ORM2 and HAC1 or a truncated intronless HAC1; PER1 and PTC2; PER1and PSE1; PER1 and UBI4; PER1 and HAC1 or a truncated intronless HAC1;PTC2 and PSE1; PTC2 and UBI4; PTC2 and HAC1 or a truncated intronlessHAC1; PSE1 and UBI4; PSE1 and HAC1 or a truncated intronless HAC1; UBI4and HAC1 or a truncated intronless HAC1; TIM9 and AHA1; TIM9 and CCT2;TIM9 and CCT3; TIM9 and CCT4; TIM9 and CCT5; TIM9 and CCT6; TIM9 andCCT7; TIM9 and CCT8; TIM9 and CNS1; TIM9 and CPR3; TIM9 and CPR6; TIM9and ERO1; TIM9 and EUG1; TIM9 and FMO1; TIM9 and HCH1; TIM9 and HSP10;TIM9 and HSP12; TIM9 and HSP104; TIM9 and HSP26; TIM9 and HSP30; TIM9and HSP42; TIM9 and HSP60; TIM9 and HSP78; TIM9 and HSP82; TIM9 andJEM1; TIM9 and MDJ1; TIM9 and MDJ2; TIM9 and MPD1; TIM9 and MPD2; TIM9and PDI1; TIM9 and PFD1; TIM9 and ABC1; TIM9 and APJ1; TIM9 and ATP11;TIM9 and ATP12; TIM9 and BTT1; TIM9 and CDC37; TIM9 and CPR7; TIM9 andHSC82; TIM9 and KAR2; TIM9 and LHS1; TIM9 and MGE1; TIM9 and MRS11; TIM9and NOB1; TIM9 and ECM10; TIM9 and SSA1; TIM9 and SSA2; TIM9 and SSA3;TIM9 and SSA4; TIM9 and SSC1; TIM9 and SSE2; TIM9 and SIL1; TIM9 andSLS1; TIM9 and ORM1; TIM9 and ORM2; TIM9 and PER1; TIM9 and PTC2; TIM9and PSE1; TIM9 and UBI4; TIM9 and HAC1 or a truncated intronless HAC1;PAM18 and AHA1; PAM18 and CCT2; PAM18 and CCT3; PAM18 and CCT4; PAM18and CCT5; PAM18 and CCT6; PAM18 and CCT7; PAM18 and CCT8; PAM18 andCNS1; PAM18 and CPR3; PAM18 and CPR6; PAM18 and ERO1; PAM18 and EUG1;PAM18 and FMO1; PAM18 and HCH1; PAM18 and HSP10; PAM18 and HSP12; PAM18and HSP104; PAM18 and HSP26; PAM18 and HSP30; PAM18 and HSP42; PAM18 andHSP60; PAM18 and HSP78; PAM18 and HSP82; PAM18 and JEM1; PAM18 and MDJ1;PAM18 and MDJ2; PAM18 and MPD1; PAM18 and MPD2; PAM18 and PDI1; PAM18and PFD1; PAM18 and ABC1; PAM18 and APJ1; PAM18 and ATP11; PAM18 andATP12; PAM18 and BTT1; PAM18 and CDC37; PAM18 and CPR7; PAM18 and HSC82;PAM18 and KAR2; PAM18 and LHS1; PAM18 and MGE1; PAM18 and MRS11; PAM18and NOB1; PAM18 and ECM10; PAM18 and SSA1; PAM18 and SSA2; PAM18 andSSA3; PAM18 and SSA4; PAM18 and SSC1; PAM18 and SSE2; PAM18 and SIL1;PAM18 and SLS1; PAM18 and ORM1; PAM18 and ORM2; PAM18 and PER1; PAM18and PTC2; PAM18 and PSE1; PAM18 and UBI4; PAM18 and HAC1 or a truncatedintronless HAC1; TCP1 and AHA1; TCP1 and CCT2; TCP1 and CCT3; TCP1 andCCT4; TCP1 and CCT5; TCP1 and CCT6; TCP1 and CCT7; TCP1 and CCT8; TCP1and CNS1; TCP1 and CPR3; TCP1 and CPR6; TCP1 and ERO1; TCP1 and EUG1;TCP1 and FMO1; TCP1 and HCH1; TCP1 and HSP10; TCP1 and HSP12; TCP1 andHSP104; TCP1 and HSP26; TCP1 and HSP30; TCP1 and HSP42; TCP1 and HSP60;TCP1 and HSP78; TCP1 and HSP82; TCP1 and JEM1; TCP1 and MDJ1; TCP1 andMDJ2; TCP1 and MPD1; TCP1 and MPD2; TCP1 and PDI1; TCP1 and PFD1; TCP1and ABC1; TCP1 and APJ1; TCP1 and ATP11; TCP1 and ATP12; TCP1 and BTT1;TCP1 and CDC37; TCP1 and CPR7; TCP1 and HSC82; TCP1 and KAR2; TCP1 andLHS1; TCP1 and MGE1; TCP1 and MRS11; TCP1 and NOB1; TCP1 and ECM10; TCP1and SSA1; TCP1 and SSA2; TCP1 and SSA3; TCP1 and SSA4; TCP1 and SSC1;TCP1 and SSE2; TCP1 and SIL1; TCP1 and SLS1; TCP1 and ORM1; TCP1 andORM2; TCP1 and PER1; TCP1 and PTC2; TCP1 and PSE1; TCP1 and UBI4; TCP1and HAC1 or a truncated intronless HAC1; TIM9 and PAM18; TIM9 and TCP1;or PAM18 and TCP1.

The first, second and third recombinant genes may, or may not, eachindividually be present on a plasmid within the host cell (which may, ormay not, be a 2 μm-family plasmid, as discussed above) or bechromosomally integrated within the genome of the host cell. It will beappreciated that any combination of plasmid and chromosomally integratedfirst, second and third recombinant genes may be used. For example, thefirst, second and third recombinant genes may, or may not, eachindividually be present on a plasmid, and this may, or may not, beeither the same plasmid or different plasmids. Alternatively, the firstrecombinant gene may, or may not, be present on a plasmid, and secondand third recombinant genes may, or may not, be chromosomally integratedwithin the genome of the host cell. Alternatively, the first and secondrecombinant genes may, or may not, be present on a plasmid and the thirdrecombinant gene may, or may not, be chromosomally integrated within thegenome of the host cell. Alternatively, the first and third recombinantgenes may, or may not, be present on a plasmid and the secondrecombinant gene may, or may not, be chromosomally integrated within thegenome of the host cell. Alternatively, the first and second recombinantgene may, or may not, be chromosomally integrated within the genome ofthe host cell and the third recombinant gene may, or may not, be presenton a plasmid. Alternatively, the first, second and third recombinantgenes may, or may not, each individually be chromosomally integratedwithin the genome of the host cell.

Plasmids used for this purpose may, or may not, be plasmids, such as 2μm-family plasmids, as defined below. Thus, in one embodiment, a methodaccording to the first aspect of the invention does not involve a hostcell in which the first, second and third recombinant genes are allpresent on the 2 μm-family plasmid.

Accordingly, as a second aspect, the present invention also provides aplasmid wherein the plasmid comprises two different genes (the first andsecond recombinant genes) encoding different chaperones. In onepreferred embodiment, the plasmid may, or may not, further comprise agene encoding a heterologous protein (the third recombinant gene), suchas a heterologous protein as described above. A plasmid according to thesecond aspect of the invention may, or may not, be a 2 μm-familyplasmid.

A third aspect of the present invention provides for the use of theplasmid of the second aspect of the invention as an expression vector toincrease the production of a desired protein, including as heterologousprotein, such as a fungal (optionally yeast) or vertebrate protein. Thedesired protein may, or may not, be encoded by a recombinant gene thatis present as part of the plasmid, or present in the host cell on adifferent plasmid, or present in the host cell as a transgene that isintegrated in the host cell's chromosome.

A fourth aspect of the invention provides a host cell comprising aplasmid as defined above. The host cell may, or may not, furthercomprise a recombinant gene encoding a desired heterologous protein.Where the recombinant gene that encodes the desired heterologous protein(the “third recombinant gene”) is not present as part of the sameplasmid that encodes the first and second chaperones, then the host cellmay, or may not, comprise the third recombinant gene on a differentplasmid, or as a transgene that is integrated in the host cell'schromosome.

As a fifth aspect, the present invention provides a host cell whichcomprises the first, second and third recombinant genes. The first,second and third recombinant genes may, or may not, each individually bepresent on a plasmid within the host cell (which may, or may not, be a 2μm-family plasmid, as discussed above) or be chromosomally integratedwithin the genome of the host cell. It will be appreciated that anycombination of plasmid and chromosomally integrated first, second andthird recombinant genes may be used, as discussed above. Thus, the hostcell may, or may not, comprise the first, second and third recombinantgenes each individually present on a plasmid, and this may, or may not,be either the same plasmid or different plasmids. Alternatively, thehost cell may, or may not, comprise the first recombinant gene on aplasmid, and second and third recombinant genes chromosomally integratedwithin the genome of the host cell.

Alternatively, the host cell may, or may not, comprise the first andsecond recombinant genes on a plasmid and the third recombinant genechromosomally integrated within the genome of the host cell.Alternatively, the host cell may, or may not, comprise the first andthird recombinant genes on a plasmid and the second recombinant genechromosomally integrated within the genome of the host cell.Alternatively, the host cell may, or may not, comprise the first andsecond recombinant genes chromosomally integrated within the genome ofthe host cell and the third recombinant gene present on a plasmid.Alternatively, the host cell may, or may not, comprise the first, secondand third recombinant genes each individually chromosomally integratedwithin the genome of the host cell.

The 2 μm-Family Plasmids:

For the purposes of the present invention, a plasmid may, or may not, bea 2 μm-family plasmid. Certain closely related species of budding yeasthave been shown to contain naturally occurring circular double strandedDNA plasmids. These plasmids, collectively termed 2 μm-family plasmids,include pSR1, pSB3 and pSB4 from Zygosaccharomyces rouxii (formerlyclassified as Zygosaccharomyces bisporus), plasmids pSB1 and pSB2 fromZygosaccharomyces bailii, plasmid pSM1 from Zygosaccharomycesfermentati, plasmid pKD1 from Kluyveromyces drosphilarum, an un-namedplasmid from Pichia membranaefaciens (hereinafter “pPM1”) and the 2 μmplasmid (such as shown in FIG. 1) and variants (such as Scp1, Scp2 andScp3) from Saccharomyces cerevisiae (Volkert, et al., 1989,Microbiological Reviews, 53, 299; Murray et al., 1988, J. Mol. Biol.200, 601; Painting, et al., 1984, J. Applied Bacteriology, 56, 331).

As a family of plasmids these molecules share a series of commonfeatures in that they typically possess two inverted repeats on oppositesides of the plasmid, have a similar size around 6-kbp (range 4757 to6615-bp), three open reading frames, one of which encodes for a sitespecific recombinase (FLP) and an autonomously replicating sequence(ARS), also known as an origin of replication (ori), located close tothe end of one of the inverted repeats. (Futcher, 1988, Yeast, 4, 27;Murray et al., op. cit., and Toh-e et al., 1986, Basic Life Sci. 40,425). Despite their lack of discernible DNA sequence homology, theirshared molecular architecture and the conservation of function of thethree open reading frames have demonstrated a common ancestral linkbetween the family members.

The above naturally occurring 2 μm-family plasmids may, or may not, beused in the present invention, but this invention is not limited to theuse of naturally occurring 2 μm-family plasmids. For the purposes ofthis invention, a 2 μm-family plasmid may, or may not, be as describedbelow.

A 2 μm-family plasmid is a circular, double stranded, DNA plasmid. It istypically small, such as between 3,000 to 10,000 bp, optionally between4,500 to 7000 bp, excluding recombinantly inserted sequences.

A 2 μm-family plasmid typically comprises at least three open readingframes (“ORFs”) that each encodes a protein that functions in the stablemaintenance of the 2 μm-family plasmid as a multicopy plasmid. Theproteins encoded by the three ORFs can be designated FLP, REP1 and REP2.Where a 2 μm-family plasmid comprises not all three of the ORFs encodingFLP, REP1 and REP2 then ORFs encoding the missing protein(s) should besupplied in trans, either on another plasmid or by chromosomalintegration.

A “FLP” protein is a protein capable of catalysing the site-specificrecombination between inverted repeat sequences recognised by FLP. Theinverted repeat sequences are termed FLP recombination target (FRT)sites and each is typically present as part of a larger inverted repeat(see below). Preferred FLP proteins comprise the sequence of the FLPproteins encoded by one of plasmids pSR1, pSB1, pSB2, pSB3, pSB4, pSM1,pKD1, pPM1 and the 2 μm plasmid, for example as described in Volkert etal, op. cit., Murray et al, op. cit., and Painting et al., op. cit.Variants and fragments of these FLP proteins are also included in thepresent invention. “Fragments” and “variants” are those which retain theability of the native protein to catalyse the site-specificrecombination between the same FRT sequences. Such variants andfragments will usually have at least 50%, 60%, 70%, 80%, 90%, 95%, 98%,99%, or more, homology with an FLP protein encoded by one of plasmidspSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 and the 2 μm plasmid.Different FLP proteins can have different FRT sequence specificities. Atypical FRT site may, or may not, comprise a core nucleotide sequenceflanked by inverted repeat sequences. In the 2 μm plasmid, the FRT coresequence is 8 nucleotides in length and the flanking inverted repeatsequences are 13 nucleotides in length (Volkert et al, op. cit.).However the FRT site recognised by any given FLP protein may, or maynot, be different to the 2 μm plasmid FRT site.

REP1 and REP2 are proteins involved in the partitioning of plasmidcopies during cell division, and may, or may not, also have a role inthe regulation of FLP expression. Considerable sequence divergence hasbeen observed between REP1 proteins from different 2 μm-family plasmids,whereas no sequence alignment is possible between REP2 proteins derivedfrom different 2 μm-family plasmids. Preferred REP1 and REP2 proteinscomprise the sequence of the REP1 and REP2 proteins encoded by one ofplasmids pSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 and the 2 μmplasmid, for example as described in Volkert et al, op. cit., Murray etal, op. cit., and Painting et al, op. cit. Variants and fragments ofthese REP1 and REP2 proteins are also included in the present invention.“Fragments” and “variants” of REP1 and REP2 are those which, whenencoded by the plasmid in place of the native ORF, do not substantiallydisrupt the stable multicopy maintenance of the plasmid within asuitable yeast population. Such variants and fragments of REP1 and REP2will usually have at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%,90%, 95%, 98%, 99%, or more, homology with a REP1 and REP2 protein,respectively, as encoded by one of plasmids pSR1, pSB1, pSB2, pSB3,pSB4, pSM1, pKD1, pPM1 and the 2 μm plasmid.

The REP1 and REP2 proteins encoded by the ORFs on the plasmid must becompatible. It is preferred that the REP1 and REP2 proteins have thesequences of REP1 and REP2 proteins encoded by the same naturallyoccurring 2 μm-family plasmid, such as pSR1, pSB1, pSB2, pSB3, pSB4,pSM1, pKD1, pPM1 and the 2 μm plasmid, or variant or fragments thereof.

A 2 μm-family plasmid typically comprises two inverted repeat sequences.The inverted repeats may be any size, so long as they each contain anFRT site (see above). The inverted repeats are typically highlyhomologous. They may, or may not, share greater than 50%, 60%, 70%, 80%,90%, 95%, 96%, 97%, 98%, 99%, 99.5% or more sequence identity. In apreferred embodiment they are identical. Typically the inverted repeatsare each between 200 to 1000 bp in length. Preferred inverted repeatsequences may, or may not, each have a length of from 200 to 300 bp, 300to 400 bp, 400 to 500 bp, 500 to 600 bp, 600 to 700 bp, 700 to 800 bp,800 to 900 bp, or 900 to 1000 bp. Particularly preferred invertedrepeats are those of the plasmids pSR1 (959 bp), pSB1 (675 bp), pSB2(477 bp), pSB3 (391 bp), pSM1 (352 bp), pKD1 (346 bp), the 2 μm plasmid(599 bp), pSB4 or pPM1.

The sequences of the inverted repeats may, or may not, be varied.However, the sequences of the FRT site in each inverted repeat should becompatible with the specificity of the FLP protein encoded by theplasmid, thereby to enable the encoded FLP protein to act to catalysethe site-specific recombination between the inverted repeat sequences ofthe plasmid. Recombination between inverted repeat sequences (and thusthe ability of the FLP protein to recognise the FRT sites with theplasmid) can be determined by methods known in the art. For example, aplasmid in a yeast cell under conditions that favour FLP expression canbe assayed for changes in the restriction profile of the plasmid whichwould result from a change in the orientation of a region of the plasmidrelative to another region of the plasmid. The detection of changes inrestriction profile indicate that the FLP protein is able to recognisethe FRT sites in the plasmid and therefore that the FRT site in eachinverted repeat are compatible with the specificity of the FLP proteinencoded by the plasmid.

In a particularly preferred embodiment, the sequences of invertedrepeats, including the FRT sites, are derived from the same 2 μm-familyplasmid as the ORF encoding the FLP protein, such as pSR1, pSB1, pSB2,pSB3, pSB4, pSM1, pKD1, pPM1 or the 2 μm plasmid.

The inverted repeats are typically positioned with the 2 μm-familyplasmid such that the two regions defined between the inverted repeats(e.g. such as defined as UL and US in the 2 μm plasmid) are ofapproximately similar size, excluding exogenously introduced sequencessuch as transgenes. For example, one of the two regions may, or may not,have a length equivalent to at least 40%, 50%, 60%, 70%, 80%, 90%, 95%or more, up to 100%, of the length of the other region.

A 2 μm-family plasmid typically comprises the ORF that encodes FLP andone inverted repeat (arbitrarily termed “IR1” to distinguish it from theother inverted repeat mentioned in the next paragraph) juxtaposed insuch a manner that IR1 occurs at the distal end of the FLP ORF, withoutany intervening coding sequence, for example as seen in the 2 μmplasmid. By “distal end” in this context we mean the end of the FLP ORFopposite to the end from which the promoter initiates its transcription.In a preferred embodiment, the distal end of the FLP ORF overlaps withIR1.

A 2 μm-family plasmid typically comprises the ORF that encodes REP2 andthe other inverted repeat (arbitrarily termed “IR2” to distinguish itfrom IR1 mentioned in the previous paragraph) juxtaposed in such amanner that IR2 occurs at the distal end of the REP2 ORF, without anyintervening coding sequence, for example as seen in the 2 μm plasmid. By“distal end” in this context we mean the end of the REP2 ORF opposite tothe end from which the promoter initiates its transcription.

In one embodiment, the ORFs encoding REP2 and FLP may, or may not, bepresent on the same region of the two regions defined between theinverted repeats of the 2 μm-family plasmid, which region may be thebigger or smaller of the regions (if there is any inequality in sizebetween the two regions).

In one embodiment, the ORFs encoding REP2 and FLP may, or may not, betranscribed from divergent promoters.

Typically, the regions defined between the inverted repeats (e.g. suchas defined as UL and US in the 2 μm plasmid) of a 2 μm-family plasmidmay, or may not, comprise not more than two endogenous genes that encodea protein that functions in the stable maintenance of the 2 μm-familyplasmid as a multicopy plasmid. Thus in a preferred embodiment, oneregion of the plasmid defined between the inverted repeats may, or maynot, comprise not more than the ORFs encoding FLP and REP2; FLP andREP1; or REP1 and REP2, as endogenous coding sequence.

A 2 μm-family plasmid typically comprises an origin of replication (alsoknown as an “autonomously replicating sequence—“ARS”), which istypically bidirectional.

Any appropriate ARS sequence can be present. Consensus sequences typicalof yeast chromosomal origins of replication may, or may not, beappropriate (Broach et al, 1982, Cold Spring Harbor Symp. Quant. Biol.,47, 1165-1174; Williamson, Yeast, 1985, 1, 1-14). Preferred ARSs includethose isolated from pSR1, pSB1, pSB2, pSB3, pSB4, pSM1, pKD1, pPM1 andthe 2 μm plasmid.

Thus, a preferred 2 μm-family plasmid may, or may not, comprise ORFsencoding FLP, REP1 and REP2, two inverted repeat sequences each invertedrepeat comprising an FRT site compatible with the encoded FLP protein,and an ARS sequence. Preferably the FRT sites are derived from the same2 μm-family plasmid as the sequence of the encoded FLP protein. Morepreferably the sequences of the encoded REP1 and REP2 proteins arederived from the same 2 μm-family plasmid as each other. Even morepreferably, the FRT sites are derived from the same 2 μm-family plasmidas the sequence of the encoded FLP, REP1 and REP2 proteins. Yet morepreferably, the sequences of the ORFs encoding FLP, REP1 and REP2, andthe sequence of the inverted repeats (including the FRT sites) arederived from the same 2 μm-family plasmid. Furthermore, the ARS sitemay, or may not, be derived from the same 2 μm-family plasmid as one ormore of the ORFs of FLP, REP1 and REP2, and the sequence of the invertedrepeats (including the FRT sites).

The term “derived from” includes sequences having an identical sequenceto the sequence from which they are derived. However, variants andfragments thereof, as defined above, are also included. For example, anFLP gene having a sequence derived from the FLP gene of the 2 μm plasmidmay, or may not, have a modified promoter or other regulatory sequencecompared to that of the naturally occurring gene. Additionally oralternatively, an FLP gene having a sequence derived from the FLP geneof the 2 μm plasmid may, or may not, have a modified nucleotide sequencein the open reading frame which may, or may not, encode the same proteinas the naturally occurring gene, or may, or may not, encode a modifiedFLP protein. The same considerations apply to other sequences on a 2μm-family plasmid having a sequence derived from a particular source.

Optionally, a 2 μm-family plasmid may, or may not, comprise a regionderived from the STB region (also known as REP3) of the 2 μm plasmid, asdefined in Volkert et al, op. cit. The STB region in a 2 μm-familyplasmid of the invention may, or may not, comprise two or more tandemrepeat sequences, such as three, four, five or more. Alternatively, notandem repeat sequences may be present. The tandem repeats may be anysize, such as 10, 20, 30, 40, 50, 60 70, 80, 90, 100 bp or more inlength. The tandem repeats in the STB region of the 2 μm plasmid are 62bp in length. It is not essential for the sequences of the tandemrepeats to be identical. Slight sequence variation can be tolerated. Itmay, or may not, be preferable to select an STB region from the sameplasmid as either or both of the REP1 and REP2 ORFs. The STB region isthought to be a cis-acting element and preferably is not transcribed.

Optionally, a 2 μm-family plasmid may, or may not, comprise anadditional ORF that encodes a protein that functions in the stablemaintenance of the 2 μm-family plasmid as a multicopy plasmid. Theadditional protein can be designated RAF or D. ORFs encoding the RAF orD gene can be seen on, for example, the 2 μm plasmid and pSM1. Thus aRAF or D ORF can comprise a sequence suitable to encode the proteinproduct of the RAF or D gene ORFs encoded by the 2 μm plasmid or pSM1,or variants and fragments thereof. Thus variants and fragments of theprotein products of the RAF or D genes of the 2 μm plasmid or pSM1 arealso included in the present invention. “Fragments” and “variants” ofthe protein products of the RAF or D genes of the 2 μm plasmid or pSM1are those which, when encoded by the 2 μm plasmid or pSM1 in place ofthe native ORF, do not disrupt the stable multicopy maintenance of theplasmid within a suitable yeast population. Such variants and fragmentswill usually have at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%,90%, 95%, 98%, 99%, or more, homology with the protein product of theRAF or D gene ORFs encoded by the 2 μm plasmid or pSM1.

A naturally occurring 2 μm-family plasmid may, or may not, be preferred.A naturally occurring 2 μm-family plasmid is any plasmid having thefeatures defined above, which plasmid is found to naturally exist inyeast, i.e. has not been recombinantly modified to include heterologoussequence. Optionally the naturally occurring 2 μm-family plasmid isselected from pSR1 (Accession No. X02398), pSB3 (Accession No. X02608)or pSB4 as obtained from Zygosaccharomyces rouxii, pSB1 or pSB2(Accession No. NC_002055 or M18274) both as obtained fromZygosaccharomyces bailli, pSM1 (Accession No. NC_002054) as obtainedfrom Zygosaccharomyces fermentati, pKD1 (Accession No. X03961) asobtained from Kluyveromyces drosophilarum, pPM1 from Pichiamembranaefaciens or, preferably, the 2 μm plasmid (Accession No.NC_001398 or J01347) as obtained from Saccharomyces cerevisiae.Accession numbers in this paragraph refer to NCBI deposits.

The 2 μm plasmid (FIG. 1) is a 6,318-bp double-stranded DNA plasmid,endogenous in most Saccharomyces cerevisiae strains at 60-100 copies perhaploid genome. The 2 μm plasmid comprises a small unique (US) regionand a large unique (UL) region, separated by two 599-bp inverted repeatsequences. Site-specific recombination of the inverted repeat sequencesresults in inter-conversion between the A-form and B-form of the plasmidin vivo (Volkert & Broach, 1986, Cell, 46, 541). The two forms of 2 μmdiffer only in the relative orientation of their unique regions.

While DNA sequencing of a cloned 2 μm plasmid (also known as Scp1) fromSaccharomyces cerevisiae gave a size of 6,318-bp (Hartley and Donelson,1980, Nature, 286, 860), other slightly smaller variants of 2 μm, Scp2and Scp3, are known to exist as a result of small deletions of 125-bpand 220-bp, respectively, in a region known as STB (Cameron et al.,1977, Nucl. Acids Res., 4, 1429: Kikuchi, 1983, Cell, 35, 487 andLivingston & Hahne, 1979, Proc. Natl. Acad. Sci. USA, 76, 3727). In onestudy about 80% of natural Saccharomyces strains from around the worldcontained DNA homologous to 2 μm (by Southern blot analysis)(Hollenberg, 1982, Current Topics in Microbiology and Immunobiology, 96,119). Furthermore, variation (genetic polymorphism) occurs within thenatural population of 2 μm plasmids found in S. cerevisiae and S.carlsbergensis, with the NCBI sequence (accession number NC_001398)being one example.

The 2 μm plasmid has a nuclear localisation and displays a high level ofmitotic stability (Mead et al, 1986, Molecular & General Genetics, 205,417). The inherent stability of the 2 μm plasmid results from aplasmid-encoded copy number amplification and partitioning mechanism,which can be compromised during the development of chimeric vectors(Futcher & Cox, 1984, J. Bacteriol., 157, 283; Bachmair & Ruis, 1984,Monatshefte für Chemie, 115, 1229). A yeast strain, which contains a 2μm plasmid is known as [cir⁺], while a yeast strain which does notcontain a 2 μm plasmid is known as [cir⁰].

The US-region of the 2 μm plasmid contains the REP2 and FLP genes, andthe UL-region contains the REP1 and D (also known as RAF) genes, theSTB-locus and the origin of replication (Broach & Hicks, 1980, Cell, 21,501; Sutton & Broach, 1985, Mol. Cell. Biol., 5, 2770). The Flprecombinase binds to FRT-sites (Flp Recognition Target) within theinverted repeats to mediate site-specific recombination, which isessential for natural plasmid amplification and control of plasmid copynumber in vivo (Senecoff et al, 1985, Proc. Natl. Acad. Sci. U.S.A., 82,7270; Jayaram, 1985, Proc. Natl. Acad. Sci. U.S.A., 82, 5875). The copynumber of 2 μm-family plasmids can be significantly affected by changesin Flp recombinase activity (Sleep et al, 2001, Yeast, 18, 403; Rose &Broach, 1990, Methods Enzymol., 185, 234). The Rep1 and Rep2 proteinsmediate plasmid segregation, although their mode of action is unclear(Sengupta et al, 2001, J. Bacteriol., 183, 2306). They also represstranscription of the FLP gene (Reynolds et al, 1987, Mol. Cell. Biol.,7, 3566).

The FLP and REP2 genes of the 2 μm plasmid are transcribed fromdivergent promoters, with apparently no intervening sequence definedbetween them. The FLP and REP2 transcripts both terminate at the samesequence motifs within the inverted repeat sequences, at 24-bp and178-bp respectively after their translation termination codons (Sutton &Broach, 1985, Mol. Cell. Biol., 5, 2770).

In the case of FLP, the C-terminal coding sequence also lies within theinverted repeat sequence. Furthermore, the two inverted repeat sequencesare highly conserved over 599-bp, a feature considered advantageous toefficient plasmid replication and amplification in vivo, although onlythe FRT-sites (less than 65-bp) are essential for site-specificrecombination in vitro (Senecoff et al, 1985, Proc. Natl. Acad. Sci.U.S.A., 82, 7270; Jayaram, 1985, Proc. Natl. Acad. Sci. U.S.A., 82,5875; Meyer-Leon et al, 1984, Cold Spring Harbor Symposia OnQuantitative Biology, 49, 797). The key catalytic residues of Flp arearginine-308 and tyrosine-343 (which is essential) with strand-cuttingfacilitated by histidine-309 and histidine 345 (Prasad et al, 1987,Proc. Natl. Acad. Sci. U.S.A., 84, 2189; Chen et al, 1992, Cell, 69,647; Grainge et al, 2001, J. Mol. Biol., 314, 717).

Two functional domains are described in Rep2. Residues 15-58 form aRep1-binding domain, and residues 59-296 contain a self-association andSTB-binding region (Sengupta et al, 2001, J. Bacteriol., 183, 2306).

Chimeric or large deletion mutant derivatives of 2 μm which lack many ofthe essential functional regions of the 2 μm plasmid but retain thefunctional cis element ARS and STB, cannot effectively partition betweenmother and daughter cells at cell division. Such plasmids can do so ifthese functions are supplied in trans, by for instance the provision ofa functional 2 μm plasmid within the host, such as a [cir⁺] host.

Genes of interest have previously been inserted into the UL-region ofthe 2 μm plasmid. For example, see plasmid pSAC3U1 in EP 0 286 424 andthe plasmid shown in FIG. 2 of WO 2005/061718, which includes aβ-lactamase gene (for ampicillin resistance), a LEU2 selectable markerand an oligonucleotide linker, the latter two of which are inserted intoa unique SnaBI-site within the UL-region of the 2 μm-like disintegrationvector, pSAC3 (see EP 0 286 424). The E. coli DNA between the XbaI-sitesthat contains the ampicillin resistance gene is lost from the plasmidshown in FIG. 2 of WO 2005/061718 after transformation into yeast. Thisis described in Chinery & Hinchliffe, 1989, Curr. Genet., 16, 21 and EP0 286 424, where these types of vectors are designated “disintegrationvectors”. Further polynucleotide insertions can be made in a NotI-sitewithin a linker (Sleep et al, 1991, Biotechnology (N.Y.), 9, 183).

Alternative insertion sites in 2 μm plasmid are known in the art,including those described in Rose & Broach (1990, Methods Enzymol., 185,234-279), such as plasmids pCV19, pCV20, CV_(neo), which utilise aninsertion at EcoRI in FLP, plasmids pCV21, pGT41 and pYE which utiliseEcoRI in D as the insertion site, plasmid pHKB52 which utilises PstI inD as the insertion site, plasmid pJDB248 which utilises an insertion atPstI in D and EcoRI in D, plasmid pJDB219 in which PstI in D and EcoRIin FLP are used as insertion sites, plasmid G18, plasmid pAB18 whichutilises an insertion at ClaI in FLP, plasmids pGT39 and pA3, plasmidspYT11, pYT14 and pYT11-LEU which use PstI in D as the insertion site,and plasmid PTY39 which uses EcoRI in FLP as the insertion site. Other 2μm plasmids include pSAC3, pSAC3U1, pSAC3U2, pSAC300, pSAC310, pSAC3C1,pSAC3PL1, pSAC3SL4, and pSAC3SC1 are described in EP 0 286 424 andChinery & Hinchliffe (1989, Curr. Genet., 16, 21-25) which alsodescribed PstI, EagI or SnaBI as appropriate 2 μm insertion sites.Further 2 μm plasmids include pAYE255, pAYE316, pAYE443, pAYE522(Kerry-Williams et al, 1998, Yeast, 14, 161-169), pDB2244 (WO 00/44772),and pAYE329 (Sleep et al, 2001, Yeast, 18, 403-421).

In one preferred embodiment, one or more genes are inserted into a 2μm-family plasmid within an untranscribed region around the ARSsequence. For example, in the 2 μm plasmid obtained from S. cerevisiae,the untranscribed region around the ARS sequence extends from the end ofthe D gene to the beginning of ARS sequence. Insertion into SnaBI (nearthe origin of replication sequence ARS) is described in Chinery &Hinchliffe, 1989, Curr. Genet., 16, 21-25. The skilled person willappreciate that gene insertions can also be made in the untranscribedregion at neighbouring positions to the SnaBI site described in Chinery& Hinchliffe.

In another preferred embodiment, REP2 and FLP genes in a 2 μm-familyplasmid each have an inverted repeat adjacent to them, and one or moregenes are inserted into a 2 μm-family plasmid within the region betweenthe first base after the last functional codon of either the REP2 geneor the FLP gene and the last base before the FRT site in the invertedrepeat adjacent to said gene. The last functional codon of either a REP2gene or a FLP gene is the codon in the open reading frame of the genethat is furthest downstream from the promoter of the gene whosereplacement by a stop codon will lead to an unacceptable loss ofmulticopy stability of the plasmid, as defined herein. Thus, disruptionof the REP2 or FLP genes at any point downstream of the last functionalcodon in either gene, by insertion of a polynucleotide sequenceinsertion, deletion or substitution will not lead to an unacceptableloss of multicopy stability of the plasmid.

For example, the REP2 gene of the 2 μm plasmid can be disrupted aftercodon 59 and that the FLP gene of the 2 μm plasmid can be disruptedafter codon 344, each without a loss of multicopy stability of theplasmid. The last functional codon in equivalent genes in other 2μm-family plasmids can be determined routinely by making mutants of theplasmids in either the FLP or REP2 genes and following the tests set outherein to determine whether the plasmid retains multicopy stability.Thus, a plasmid insertion site as defined in WO 2005/061719 may, or maynot, be used to carry one or more a recombinant genes according to anyaspect of the present invention.

One can determine whether a plasmid retains multicopy stability usingtest such as defined in Chinery & Hinchliffe (1989, Curr. Genet., 16,21-25). For yeast that do not grow in the non-selective media (YPD, alsodesignated YEPD) defined in Chinery & Hinchliffe (1989, Curr. Genet.,16, 21-25) other appropriate non-selective media might be used. Plasmidstability may be defined as the percentage cells remaining prototrophicfor the selectable marker after a defined number of generations. Thenumber of generations will preferably be sufficient to show a differencebetween a control plasmid, such as pSAC35 or pSAC310, or to showncomparable stability to such a control plasmid. The number ofgenerations may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or more.Higher numbers are preferred. The acceptable plasmid stability might be1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%,80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9% or substantially 100%.Higher percentages are preferred. The skilled person will appreciatethat, even though a plasmid may have a stability less than 100% whengrown on non-selective media, that plasmid can still be of use whencultured in selective media. For example plasmid pDB2711 as described inthe examples is only 10% stable when the stability is determinedaccordingly to test of Example 2 of WO 2005/061719, but provides a15-fold increase in recombinant transferrin productivity in shake flaskculture under selective growth conditions.

Thus one or more gene insertions may, or may not, occur between thefirst base after the last functional codon of the REP2 gene and the lastbase before the FRT site in an inverted repeat adjacent to said gene,preferably between the first base of the inverted repeat and the lastbase before the FRT site, more preferably at a position after thetranslation termination codon of the REP2 gene and before the last basebefore the FRT site.

Additionally or alternatively one or more gene insertions may, or maynot, occur between the first base after the last functional codon of theFLP gene and the last base before the FRT site in an inverted repeatadjacent to said gene, preferably between the first base of the invertedrepeat and the last base before the FRT site, more preferably betweenthe first base after the end of the FLP coding sequence and the lastbase before the FRT site, such as at the first base after the end of theFLP coding sequence.

In one preferred embodiment, where the 2 μm-family plasmid is based onthe 2 μm plasmid of S. cerevisiae, it is a disintegration vector asknown in the art (for example, see EP 286 424, the contents of which areincorporated herein by reference). A disintegration vector may, or maynot, be a 2 μm plasmid vector comprising a DNA sequence which isintended to be lost by recombination, three 2 μm FRT sites, of which onepair of sites is in direct orientation and the other two pairs are inindirect orientation, and a DNA sequence of interest (such as an E. coliorigin of replication and bacterial selectable marker), the saidsequence to be lost being located between the said sites which are indirect orientation.

Thus, the sequence to be lost may, or may not, comprise a selectablemarker DNA sequence.

A preferred disintegration vector may, or may not, comprise a complete 2μm plasmid additionally carrying (i) a bacterial plasmid DNA sequencenecessary for propagation of the vector in a bacterial host; (ii) anextra 2 μm FRT site; and a selectable marker DNA sequence for yeasttransformation; the said bacterial plasmid DNA sequence being presentand the extra FRT site being created at a restriction site, such asXbaI, in one of the two inverted repeat sequences of the 2 μm plasmid,the said extra FRT site being in direct orientation in relation to theendogenous FRT site of the said one repeat sequence, and the bacterialplasmid DNA sequence being sandwiched between the extra FRT site and theendogenous FRT site of the said one repeat sequence. In a preferreddisintegration vector, all bacterial plasmid DNA sequences may, or maynot, be sandwiched as said. A particularly preferred 2 μm plasmid vectorhas substantially the configuration of pSAC3 as shown in EP 286 424.

The term “disintegration vector” as used herein also includes plasmidsas defined in U.S. Pat. No. 6,451,559, the contents of which areincorporated herein by reference. Thus a disintegration vector may, ormay not, be a 2 μm vector that, other than DNA sequence encodingnon-yeast polypeptides, contains no bacterial (particularly E. coli)origin of replication, or more preferably no bacterial (particularly E.coli) sequence and preferably all DNA in said vector, other than DNAsequence encoding non-yeast polypeptides, is yeast-derived DNA.

Desired Proteins and Other Proteins Defined by the Present Application:

The terms “protein” and “desired protein” as used herein includes allnatural and non-natural proteins, polypeptides and peptides. For thepurposes of the present invention, a “heterologous protein” is a proteinthat is encoded by a “recombinant gene” as described above. The“heterologous protein” may, or may not, be identical in sequence to aprotein that is encoded by one of more other genes that naturally occurin the expression system that is used (by “expression system” we includethe meaning of a host cell's genome (typically the chromosome) where the“recombinant gene” is chromosomally integrated, or a plasmid where the“recombinant gene” is encoded by a plasmid). For example, in the contextof a “heterologous protein” that is encoded by a “recombinant gene”carried on a 2 μm-family plasmid, the “heterologous protein” may, or maynot, be a protein that is not naturally encoded by a 2 μm-family plasmidand can also be described as a “non 2 μm-family plasmid protein”. Forconvenience, the terms “heterologous protein” and “non 2 μm-familyplasmid protein” are used synonymously in this application. Optionallytherefore, when encoded by a 2 μm-family, the heterologous protein isnot a FLP, REP1, REP2, or a RAF/D protein as encoded by any one of pSR1,pSB3 or pSB4 as obtained from Z. rouxii, pSB1 or pSB2 both as obtainedfrom Z. bailli, pSM1 as obtained from Z. fermentati, pKD1 as obtainedfrom K. drosophilarum, pPM1 as obtained from P. membranaefaciens or the2 μm plasmid as obtained from S. cerevisiae.

A gene encoding a desired heterologous, or other, protein comprises apolynucleotide sequence encoding the heterologous protein (typicallyaccording to standard codon usage for any given organism), designatedthe open reading frame (“ORF”). The gene may, or may not, additionallycomprise some polynucleotide sequence that does not encode an openreading frame (termed “non-coding region”).

Non-coding region in the gene may, or may not, contain one or moreregulatory sequences, operatively linked to the ORF, which allow for thetranscription of the open reading frame and/or translation of theresultant transcript.

The term “regulatory sequence” refers to a sequence that modulates(i.e., promotes or reduces) the expression (i.e., the transcriptionand/or translation) of an ORF to which it is operably linked. Regulatoryregions typically include promoters, terminators, ribosome binding sitesand the like. The skilled person will appreciate that the choice ofregulatory region will depend upon the intended expression system. Forexample, promoters may, or may not, be constitutive or inducible andmay, or may not, be cell- or tissue-type specific or non-specific.

Suitable regulatory regions, may, or may not, be 5 bp, 10 bp, 15 bp, 20bp, 25 bp, 30 bp, 35 bp, 40 bp, 45 bp, 50 bp, 60 bp, 70 bp, 80 bp, 90bp, 100 bp, 120 bp, 140 bp, 160 bp, 180 bp, 200 bp, 220 bp, 240 bp, 260bp, 280 bp, 300 bp, 350 bp, 400 bp, 450 bp, 500 bp, 550 bp, 600 bp, 650bp, 700 bp, 750 bp, 800 bp, 850 bp, 900 bp, 950 bp, 1000 bp, 1100 bp,1200 bp, 1300 bp, 1400 bp, 1500 bp or greater, in length.

Those skilled in the art will recognise that the gene encoding achaperone, for example PDI, may, or may not, additionally comprisenon-coding regions and/or regulatory regions. Such non-coding regionsand regulatory regions are not restricted to the native non-codingregions and/or regulatory regions normally associated with the chaperoneORF.

Where the expression system is yeast, such as Saccharomyces cerevisiae,suitable promoters for S. cerevisiae include those associated with thePGK1 gene, GAL1 or GAL10 genes, TEF1, TEF2, PYK1, PMA1, CYC1, PHO5,TRP1, ADH1, ADH2, the genes for glyceraldehyde-3-phosphatedehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase,triose phosphate isomerase, phosphoglucose isomerase, glucokinase,α-mating factor pheromone, α-mating factor pheromone, the PRB1 promoter,the PRA1 promoter, the GPD1 promoter, and hybrid promoters involvinghybrids of parts of 5′ regulatory regions with parts of 5′ regulatoryregions of other promoters or with upstream activation sites (e.g. thepromoter of EP-A-258 067).

Suitable transcription termination signals are well known in the art.Where the host cell is eucaryotic, the transcription termination signalis optionally derived from the 3′ flanking sequence of a eucaryoticgene, which contains proper signals for transcription termination andpolyadenylation. Suitable 3′ flanking sequences may, or may not, forexample, be those of the gene naturally linked to the expression controlsequence used, i.e. may, or may not, correspond to the promoter.Alternatively, they may be different. In that case, and where the hostis a yeast, optionally S. cerevisiae, then the termination signal of theS. cerevisiae ADH1, ADH2, CYC1, or PGK1 genes are preferred.

It may, or may not, be beneficial for the promoter and open readingframe of the gene, such as a gene encoding the chaperone (e.g. PDI1) ora desired protein (such as a heterologous desired protein), to beflanked by transcription termination sequences so that the transcriptiontermination sequences are located both upstream and downstream of thepromoter and open reading frame, in order to prevent transcriptionalread-through into neighbouring genes, such as 2 μm genes, and viceversa.

In one embodiment, the favoured regulatory sequences in yeast, such asSaccharomyces cerevisiae, include: a yeast promoter (e.g. theSaccharomyces cerevisiae PRB1 promoter), as taught in EP 431 880; and atranscription terminator, optionally the terminator from SaccharomycesADH1, as taught in EP 60 057. Optionally, the vector incorporates atleast two translation stop codons.

It may, or may not, be beneficial for the non-coding region toincorporate more than one DNA sequence encoding a translational stopcodon, such as UAA, UAG or UGA, in order to minimise translationalread-through and thus avoid the production of elongated, non-naturalfusion proteins. The translation stop codon UAA is preferred.

The term “operably linked” includes within its meaning that a regulatorysequence is positioned within any non-coding region in a gene such thatit forms a relationship with an ORF that permits the regulatory regionto exert an effect on the ORF in its intended manner. Thus a regulatoryregion “operably linked” to an ORF is positioned in such a way that theregulatory region is able to influence transcription and/or translationof the ORF in the intended manner, under conditions compatible with theregulatory sequence.

In one preferred embodiment, the desired protein (such as theheterologous desired protein) is secreted. In that case, a sequenceencoding a secretion leader sequence which, for example, comprises mostof the natural HSA secretion leader, plus a small portion of the S.cerevisiae α-mating factor secretion leader as taught in WO 90/01063may, or may not, be included in the open reading frame.

Alternatively, the desired protein (such as a heterologous desiredprotein) may, or may not, be intracellular.

The desired protein (such as a heterologous desired protein) may, or maynot, comprise the sequence of a eucaryotic protein, or a fragment orvariant thereof. Suitable eucaryotes include fungi, plants and animals.In one embodiment the heterologous protein may, or may not, be a fungalprotein, such as a yeast protein. In another preferred embodiment thedesired protein (such as a heterologous desired protein) may, or maynot, be an animal protein. Exemplary animals include vertebrates andinvertebrates. Exemplary vertebrates include mammals, such as humans,and non-human mammals.

Thus the desired protein (such as a heterologous desired protein) may,or may not, comprise the sequence of a yeast protein. It may, or maynot, for example, comprise the sequence of a yeast protein from the samehost from which a 2 μm-family plasmid is derived, particularly if thegene encoding the heterologous protein is integrated into said 2μm-family plasmid. Those skilled in the art will recognise that amethod, use or plasmid of the invention may, or may not, comprise DNAsequences encoding more than one heterologous protein, more than onechaperone, or more than one heterologous protein and more than onechaperone.

In another embodiment, the desired protein (such as a desiredheterologous protein) may, or may not, comprise the sequence of albumin,a monoclonal antibody, an etoposide, a serum protein (such as a bloodclotting factor), antistasin, a tick anticoagulant peptide, transferrin,lactoferrin, endostatin, angiostatin, collagens, immunoglobulins orimmunoglobulin-based molecules or fragment of either (e.g. a SmallModular ImmunoPharmaceutical™ (“SMIP”) or dAb, Fab′ fragments, F(ab′)2,scAb, scFv or scFv fragment), a Kunitz domain protein (such as thosedescribed in WO 03/066824, with or without albumin fusions),interferons, interleukins, IL10, IL11, IL2, interferon α species andsub-species, interferon β species and sub-species, interferon γ speciesand sub-species, leptin, CNTF, CNTF_(Ax15), IL1-receptor antagonist,erythropoietin (EPO) and EPO mimics, thrombopoietin (TPO) and TPOmimics, prosaptide, cyanovirin-N, 5-helix, T20 peptide, T1249 peptide,HIV gp41, HIV gp120, urokinase, prourokinase, tPA, hirudin, plateletderived growth factor, parathyroid hormone, proinsulin, insulin,glucagon, glucagon-like peptides, insulin-like growth factor,calcitonin, growth hormone, transforming growth factor β, tumournecrosis factor, G-CSF, GM-CSF, M-CSF, FGF, coagulation factors in bothpre and active forms, including but not limited to plasminogen,fibrinogen, thrombin, pre-thrombin, pro-thrombin, von Willebrand'sfactor, α₁-antitrypsin, plasminogen activators, Factor VII, Factor VIII,Factor IX, Factor X and Factor XIII, nerve growth factor, LACI,platelet-derived endothelial cell growth factor (PD-ECGF), glucoseoxidase, serum cholinesterase, aprotinin, amyloid precursor protein,inter-alpha trypsin inhibitor, antithrombin III, apo-lipoproteinspecies, Protein C, Protein S, a metabolite, an antibiotic, or a variantor fragment of any of the above.

A “variant”, in the context of the above-listed proteins, refers to aprotein wherein at one or more positions there have been amino acidinsertions, deletions, or substitutions, either conservative ornon-conservative, provided that such changes result in a protein whosebasic properties, for example enzymatic activity or receptor binding(type of and specific activity), thermostability, activity in a certainpH-range (pH-stability) have not significantly been changed.“Significantly” in this context means that one skilled in the art wouldsay that the properties of the variant may still be different but wouldnot be unobvious over the ones of the original protein.

By “conservative substitutions” is intended combinations such as Val,Ile, Leu, Ala, Met; Asp, Glu; Asn, Gln; Ser, Thr, Gly, Ala; Lys, Arg,His; and Phe, Tyr, Trp. Preferred conservative substitutions includeGly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; andPhe, Tyr.

A “variant” typically has at least 25%, at least 50%, at least 60% or atleast 70%, preferably at least 80%, more preferably at least 90%, evenmore preferably at least 95%, yet more preferably at least 99%, mostpreferably at least 99.5% sequence identity to the polypeptide fromwhich it is derived.

The percent sequence identity between two polypeptides may be determinedusing suitable computer programs, for example the GAP program of theUniversity of Wisconsin Genetic Computing Group and it will beappreciated that percent identity is calculated in relation topolypeptides whose sequence has been aligned optimally.

The alignment may alternatively be carried out using the Clustal Wprogram (Thompson et al., (1994) Nucleic Acids Res., 22(22), 4673-80).The parameters used may, or may not, be as follows:

-   -   Fast pairwise alignment parameters: K-tuple(word) size; 1,        window size; 5, gap penalty; 3, number of top diagonals; 5.        Scoring method: x percent.    -   Multiple alignment parameters: gap open penalty; 10, gap        extension penalty; 0.05.    -   Scoring matrix: BLOSUM.

Such variants may, or may not, be natural or made using the methods ofprotein engineering and site-directed mutagenesis as are well known inthe art.

A “fragment”, in the context of the above-listed proteins, refers to aprotein wherein at one or more positions there have been deletions. Thusthe fragment may, or may not, comprise at most 5, 10, 20, 30, 40 or 50%of the complete sequence of the full mature polypeptide. Typically afragment comprises up to 60%, more typically up to 70%, preferably up to80%, more preferably up to 90%, even more preferably up to 95%, yet morepreferably up to 99% of the complete sequence of the full desiredprotein. Particularly preferred fragments of a protein comprise one ormore whole domains of the protein.

In one particularly preferred embodiment the desired protein (such as adesired heterologous protein) comprises the sequence of albumin or avariant or fragment thereof.

By “albumin” we include a protein comprising the sequence of an albuminprotein obtained from any source. Typically the source is mammalian. Inone preferred embodiment the serum albumin is human serum albumin(“HSA”). The term “human serum albumin” includes the meaning of a serumalbumin having an amino acid sequence naturally occurring in humans, andvariants thereof. Optionally the albumin has the amino acid sequencedisclosed in WO 90/13653 or a variant thereof. The HSA coding sequenceis obtainable by known methods for isolating cDNA corresponding to humangenes, and is also disclosed in, for example, EP 73 646 and EP 286 424.

In another preferred embodiment the “albumin” comprises the sequence ofbovine serum albumin. The term “bovine serum albumin” includes themeaning of a serum albumin having an amino acid sequence naturallyoccurring in cows, for example as taken from Swissprot accession numberP02769, and variants thereof as defined below. The term “bovine serumalbumin” also includes the meaning of fragments of full-length bovineserum albumin or variants thereof, as defined below.

In another preferred embodiment the albumin comprises the sequence of analbumin derived from one of serum albumin from dog (e.g. see Swissprotaccession number P49822), pig (e.g. see Swissprot accession numberP08835), goat (e.g. as available from Sigma as product no. A2514 orA4164), turkey (e.g. see Swissprot accession number O73860), baboon(e.g. as available from Sigma as product no. A1516), cat (e.g. seeSwissprot accession number P49064), chicken (e.g. see Swissprotaccession number P19121), ovalbumin (e.g. chicken ovalbumin) (e.g. seeSwissprot accession number P01012), donkey (e.g. see Swissprot accessionnumber P39090), guinea pig (e.g. as available from Sigma as product no.A3060, A2639, 05483 or A6539), hamster (e.g. as available from Sigma asproduct no. A5409), horse (e.g. see Swissprot accession number P35747),rhesus monkey (e.g. see Swissprot accession number Q28522), mouse (e.g.see Swissprot accession number 089020), pigeon (e.g. as defined by Khanet al, 2002, Int. J. Biol. Macromol., 30(3-4), 171-8), rabbit (e.g. seeSwissprot accession number P49065), rat (e.g. see Swissprot accessionnumber P36953) and sheep (e.g. see Swissprot accession number P14639)and includes variants and fragments thereof as defined below.

Many naturally occurring mutant forms of albumin are known. Many aredescribed in Peters, (1996, All About Albumin: Biochemistry, Geneticsand Medical Applications, Academic Press, Inc., San Diego, Calif., p.170-181). A variant as defined above may, or may not, be one of thesenaturally occurring mutants.

A “variant albumin” refers to an albumin protein wherein at one or morepositions there have been amino acid insertions, deletions, orsubstitutions, either conservative or non-conservative, provided thatsuch changes result in an albumin protein for which at least one basicproperty, for example binding activity (type of and specific activitye.g. binding to bilirubin), osmolarity (oncotic pressure, colloidosmotic pressure), behaviour in a certain pH-range (pH-stability) hasnot significantly been changed. “Significantly” in this context meansthat one skilled in the art would say that the properties of the variantmay still be different but would not be unobvious over the ones of theoriginal protein.

By “conservative substitutions” is intended combinations such as Gly,Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe,Tyr. Such variants may, or may not, be made by techniques well known inthe art, such as by site-directed mutagenesis as disclosed in U.S. Pat.No. 4,302,386 issued 24 Nov. 1981 to Stevens, incorporated herein byreference.

Typically an albumin variant will have more than 40%, usually at least50%, more typically at least 60%, preferably at least 70%, morepreferably at least 80%, yet more preferably at least 90%, even morepreferably at least 95%, most preferably at least 98% or more sequenceidentity with naturally occurring albumin. The percent sequence identitybetween two polypeptides may be determined using suitable computerprograms, for example the GAP program of the University of WisconsinGenetic Computing Group and it will be appreciated that percent identityis calculated in relation to polypeptides whose sequence has beenaligned optimally. The alignment may alternatively be carried out usingthe Clustal W program (Thompson et al., 1994). The parameters used may,or may not, be as follows:

Fast pairwise alignment parameters: K-tuple(word) size; 1, window size;5, gap penalty; 3, number of top diagonals; 5. Scoring method: xpercent. Multiple alignment parameters: gap open penalty; 10, gapextension penalty; 0.05. Scoring matrix: BLOSUM.

The term “fragment” as used above includes any fragment of full-lengthalbumin or a variant thereof, so long as at least one basic property,for example binding activity (type of and specific activity e.g. bindingto bilirubin), osmolarity (oncotic pressure, colloid osmotic pressure),behaviour in a certain pH-range (pH-stability) has not significantlybeen changed. “Significantly” in this context means that one skilled inthe art would say that the properties of the variant may still bedifferent but would not be unobvious over the ones of the originalprotein. A fragment will typically be at least 50 amino acids long. Afragment may, or may not, comprise at least one whole sub-domain ofalbumin. Domains of HSA have been expressed as recombinant proteins(Dockal, M. et al., 1999, J. Biol. Chem., 274, 29303-29310), wheredomain I was defined as consisting of amino acids 1-197, domain II wasdefined as consisting of amino acids 189-385 and domain III was definedas consisting of amino acids 381-585. Partial overlap of the domainsoccurs because of the extended α-helix structure (h10-h1) which existsbetween domains I and II, and between domains II and III (Peters, 1996,op. cit., Table 2-4). HSA also comprises six sub-domains (sub-domainsIA, IB, HA, IIB, IIIA and IIIB). Sub-domain IA comprises amino acids6-105, sub-domain IB comprises amino acids 120-177, sub-domain IIAcomprises amino acids 200-291, sub-domain IIB comprises amino acids316-369, sub-domain IIIA comprises amino acids 392-491 and sub-domainIIIB comprises amino acids 512-583. A fragment may, or may not, comprisea whole or part of one or more domains or sub-domains as defined above,or any combination of those domains and/or sub-domains.

In another particularly preferred embodiment the desired protein (suchas a desired heterologous protein) comprises the sequence of transferrinor a variant or fragment thereof. The term “transferrin” as used hereinincludes all members of the transferrin family (Testa, Proteins of ironmetabolism, CRC Press, 2002; Harris & Aisen, Iron carriers and ironproteins, Vol. 5, Physical Bioinorganic Chemistry, V C H, 1991) andtheir derivatives, such as transferrin, mutant transferrins (Mason etal, 1993, Biochemistry, 32, 5472; Mason et al, 1998, Biochem. J.,330(1), 35), truncated transferrins, transferrin lobes (Mason et al,1996, Protein Expr. Purif., 8, 119; Mason et al, 1991, Protein Expr.Purif., 2, 214), lactoferrin, mutant lactoferrins, truncatedlactoferrins, lactoferrin lobes or fusions of any of the above to otherpeptides, polypeptides or proteins (Shin et al, 1995, Proc. Natl. Acad.Sci. USA, 92, 2820; Ali et al, 1999, J. Biol. Chem., 274, 24066; Masonet al, 2002, Biochemistry, 41, 9448).

The transferrin may, or may not, be human transferrin. The term “humantransferrin” is used herein to denote material which isindistinguishable from transferrin derived from a human or which is avariant or fragment thereof. A “variant” includes insertions, deletionsand substitutions, either conservative or non-conservative, where suchchanges do not substantially alter the useful ligand-binding orimmunogenic properties of transferrin.

Mutants of transferrin are included in the invention. Such mutants may,or may not, have altered immunogenicity. For example, transferrinmutants may, or may not, display modified (e.g. reduced) glycosylation.The N-linked glycosylation pattern of a transferrin molecule can bemodified by adding/removing amino acid glycosylation consensus sequencessuch as N-X-S/T, at any or all of the N, X, or S/T position. Transferrinmutants may, or may not, be altered in their natural binding to metalions and/or other proteins, such as transferrin receptor. An example ofa transferrin mutant modified in this manner is exemplified below.

We also include naturally-occurring polymorphic variants of humantransferrin or human transferrin analogues. Generally, variants orfragments of human transferrin will have at least 5%, 10%, 15%, 20%,30%, 40% or 50% (preferably at least 80%, 90% or 95%) of humantransferrin's ligand binding activity (for example iron-binding), weightfor weight. The iron binding activity of transferrin or a test samplecan be determined spectrophotometrically by 470 nm:280 nm absorbanceratios for the proteins in their iron-free and fully iron-loaded states.Reagents should be iron-free unless stated otherwise. Iron can beremoved from transferrin or the test sample by dialysis against 0.1Mcitrate, 0.1M acetate, 10 mM EDTA pH4.5. Protein should be atapproximately 20 mg/mL in 100 mM HEPES, 10 mM NaHCO₃ pH8.0. Measure the470 nm:280 nm absorbance ratio of apo-transferrin (Calbiochem, CNBiosciences, Nottingham, UK) diluted in water so that absorbance at 280nm can be accurately determined spectrophotometrically (0% ironbinding). Prepare 20 mM iron-nitrilotriacetate (FeNTA) solution bydissolving 191 mg nitrotriacetic acid in 2 mL 1M NaOH, then add 2 mL0.5M ferric chloride. Dilute to 50 mL with deionised water. Fully loadapo-transferrin with iron (100% iron binding) by adding a sufficientexcess of freshly prepared 20 mM FeNTA, then dialyse theholo-transferrin preparation completely against 100 mM HEPES, 10 mMNaHCO₃ pH8.0 to remove remaining FeNTA before measuring the absorbanceratio at 470 nm:280 nm. Repeat the procedure using test sample, whichshould initially be free from iron, and compare final ratios to thecontrol.

Additionally, single or multiple heterologous fusions comprising any ofthe above; or single or multiple heterologous fusions to albumin,transferrin or immunoglobins or a variant or fragment of any of thesemay, or may not, be used. Such fusions include albumin N-terminalfusions, albumin C-terminal fusions and co-N-terminal and C-terminalalbumin fusions as exemplified by WO 01/79271, and transferrinN-terminal fusions, transferrin C-terminal fusions, and co-N-terminaland C-terminal transferrin fusions.

Examples of transferrin fusions are given in US patent applicationsUS2003/0221201 and US2003/0226155, Shin, et al., 1995, Proc Natl AcadSci USA, 92, 2820, Ali, et al., 1999, J Biol Chem, 274, 24066, Mason, etal., 2002, Biochemistry, 41, 9448, the contents of which areincorporated herein by reference.

The skilled person will also appreciate that the open reading frame ofany other gene or variant, or part or either, can be utilised as an openreading frame for use with the present invention. For example, the openreading frame may, or may not, encode a protein comprising any sequence,be it a natural protein (including a zymogen), or a variant, or afragment (which may, or may not, for example, be a domain) of a naturalprotein; or a totally synthetic protein; or a single or multiple fusionof different proteins (natural or synthetic). Such proteins can betaken, but not exclusively, from the lists provided in WO 01/79258, WO01/79271, WO 01/79442, WO 01/79443, WO 01/79444 and WO 01/79480, or avariant or fragment thereof; the disclosures of which are incorporatedherein by reference. Although these patent applications present the listof proteins in the context of fusion partners for albumin, the presentinvention is not so limited and, for the purposes of the presentinvention, any of the proteins listed therein may, or may not, bepresented alone or as fusion partners for albumin, the Fc region ofimmunoglobulin, transferrin, lactoferrin or any other protein orfragment or variant of any of the above, as a desired polypeptide.

The desired protein (such as a desired heterologous protein) may, or maynot, be a therapeutically active protein. In other words, it may, or maynot, have a recognised medical effect on individuals, such as humans.Many different types of therapeutically active protein are well known inthe art.

The desired protein (such as a desired heterologous protein) may, or maynot, be a protein that is useful in diagnostic techniques. Manydifferent types of diagnostically useful protein are well known in theart.

The desired protein (such as a desired heterologous protein) may, or maynot, be a protein that has no relationship to healthcare. It may, or maynot, for example, be a protein that has a utility as an industrial,domestic or nutritional (e.g. as a foodstuff or additive) agent. Manydifferent types of proteins having industrial, domestic and/ornutritional utilities are also well known in the art.

The desired protein (such as a desired heterologous protein) may, or maynot, comprise a leader sequence effective to cause secretion in a hostcell, such as in a yeast cell.

Numerous natural or artificial polypeptide signal sequences (also calledsecretion pre regions) have been used or developed for secretingproteins from host cells. The signal sequence directs the nascentprotein towards the machinery of the cell that exports proteins from thecell into the surrounding medium or, in some cases, into the periplasmicspace. The signal sequence is usually, although not necessarily, locatedat the N-terminus of the primary translation product and is generally,although not necessarily, cleaved off the protein during the secretionprocess, to yield the “mature” protein.

In the case of some proteins the entity that is initially secreted,after the removal of the signal sequence, includes additional aminoacids at its N-terminus called a “pro” sequence, the intermediate entitybeing called a “pro-protein”. These pro sequences may, or may not,assist the final protein to fold and become functional, and are usuallythen cleaved off. In other instances, the pro region simply provides acleavage site for an enzyme to cleave off the pre-pro region and is notknown to have another function.

The pro sequence can be removed either during the secretion of theprotein from the cell or after export from the cell into the surroundingmedium or periplasmic space.

Polypeptide sequences which direct the secretion of proteins, whetherthey resemble signal (i.e. pre) sequences or pre-pro secretionsequences, are referred to as leader sequences. The secretion ofproteins is a dynamic process involving translation, translocation andpost-translational processing, and one or more of these steps may notnecessarily be completed before another is either initiated orcompleted.

For production of proteins in eucaryotic species such as the yeastsSaccharomyces cerevisiae, Zygosaccharomyces species, Kluyveromyceslactis and Pichia pastoris, known leader sequences include those fromthe S. cerevisiae acid phosphatase protein (Pho5p) (see EP 366 400), theinvertase protein (Suc2p) (see Smith et al. (1985) Science, 229,1219-1224) and heat-shock protein-150 (Hsp150p) (see WO 95/33833).Additionally, leader sequences from the S. cerevisiae mating factoralpha-1 protein (MFα-1) and from the human lysozyme and human serumalbumin (HSA) protein have been used, the latter having been usedespecially, although not exclusively, for secreting human albumin. WO90/01063 discloses a fusion of the MFα-1 and HSA leader sequences, whichadvantageously reduces the production of a contaminating fragment ofhuman albumin relative to the use of the MFα-1 leader sequence. Modifiedleader sequences are also disclosed in WO 2004/009819 and in theexamples of this application; the reader will appreciate that thoseleader sequences can be used with proteins other than transferrin. Inaddition, the natural transferrin leader sequence may, or may not, beused to direct secretion of transferrin and other heterologous proteins.

Where a chaperone that is recombinantly expressed according to thepresent invention is protein disulphide isomerase, then optionally thedesired protein (such as a desired heterologous protein) may, or maynot, comprise disulphide bonds in its mature form. Any disulphide bondsmay, or may not, be intramolecular and/or intermolecular.

The desired protein (such as a desired heterologous protein) may, or maynot, be a commercially useful protein, such as a therapeutically,diagnostically, industrially, domestically or nutritionally usefulprotein. Some proteins, such as heterologously expressed proteins, areintended to interact with the cell in which they are expressed in orderto bring about a beneficial effect on the cell's activities. Theseproteins are not, in their own right, commercially useful. Commerciallyuseful proteins are proteins that have a utility ex vivo of the cell inwhich they are expressed. Nevertheless, the skilled reader willappreciate that a commercially useful protein may, or may not, also havea biological effect on the host cell expressing it (such as aheterologous protein), but that that effect is not the main or solereason for expressing the protein therein.

Commercially useful proteins may include proteins that are useful asmetabolites or antibiotics, and the like.

In one embodiment it is preferred that the desired protein (such as adesired heterologous protein) is not β-lactamase. In another embodimentit is preferred that the desired protein (such as a desired heterologousprotein) is not antistasin. However, the reader will appreciate thatneither of these provisos exclude genes encoding either β-lactamase orantistasin from being present in a host cell or on a plasmid of theinvention, merely that the gene encoding the desired protein (such as adesired heterologous protein) encodes a protein other than β-lactamaseand/or antistasin.

Plasmids useful in the practice of the present invention can, unlessspecified otherwise, be any type of plasmid. For the purposes of thepresent invention, references to “plasmids” may, or may not, alsoinclude a reference to other types of vectors. It may be appropriate tochoose a suitable plasmid based on the host cell system in which it willbe used.

Many plasmids and other vectors are known for the transformation ofvarious expression systems, including systems employing: bacteria (e.g.Bacillus subtilis or Escherichia coli) transformed with, for example,recombinant bacteriophage, plasmid or cosmid DNA expression vectors;yeasts (e.g. Saccharomyces cerevisiae or Pichia pastoris) transformedwith, for example, yeast expression vectors; insect cell systemstransformed with, for example, viral expression vectors (e.g.baculovirus); plant cell systems transfected with, for example viral orbacterial expression vectors; animal cell systems, either in cellculture, transgenic or as gene therapy, transfected with, for example,adenovirus expression vectors.

Typical procaryotic vector plasmids are: pUC18, pUC19, pBR322 and pBR329available from Biorad Laboratories (Richmond, Calif., USA); pTrc99A,pKK223-3, pKK233-3, pDR540 and pRIT5 available from Pharmacia(Piscataway, N.J., USA); pBS vectors, Phagescript vectors, Bluescriptvectors, pNH8A, pNH16A, pNH18A, pNH46A available from Stratagene CloningSystems (La Jolla, Calif. 92037, USA).

A typical mammalian cell vector plasmid is pSVL available from Pharmacia(Piscataway, N.J., USA). This vector uses the SV40 late promoter todrive expression of cloned genes, the highest level of expression beingfound in T antigen-producing cells, such as COS-1 cells. An example ofan inducible mammalian expression vector is pMSG, also available fromPharmacia (Piscataway, N.J., USA). This vector uses theglucocorticoid-inducible promoter of the mouse mammary tumour virus longterminal repeat to drive expression of the cloned gene.

Useful yeast plasmid vectors include the 2 μm-family plasmids (asdescribed above), as well as pRS403-406 and pRS413-416 which aregenerally available from Stratagene Cloning Systems (La Jolla, Calif.92037, USA). Plasmids pRS403, pRS404, pRS405 and pRS406 are YeastIntegrating plasmids (Yips) and incorporate the yeast selectable markersHIS3, TRP1, LEU2 and URA3. Plasmids pRS413-416 are Yeast Centromereplasmids (YCps). Other YIps and YCps plasmids may also be used.

Plasmids for use in any aspect of the present invention can be preparedby modifying plasmids, such as 2 μm-family plasmids, known in the art byinserting the required sequences (for example, one or more genesencoding chaperones and/or one or more genes encoding a heterologousprotein) using techniques well known in the art such as are described inby Sambrook et al., Molecular Cloning: A Laboratory Manual, 2001, 3rdedition, the contents of which are incorporated herein by reference. Forexample, one such method involves ligation via cohesive ends. Compatiblecohesive ends can be generated on a DNA fragment for insertion andplasmid by the action of suitable restriction enzymes. These ends willrapidly anneal through complementary base pairing and remaining nickscan be closed by the action of DNA ligase.

A further method uses synthetic double stranded oligonucleotide linkersand adaptors. DNA fragments with blunt ends are generated bybacteriophage T4 DNA polymerase or E. coli DNA polymerase I which removeprotruding 3′ termini and fill in recessed 3′ ends. Synthetic linkersand pieces of blunt-ended double-stranded DNA, which contain recognitionsequences for defined restriction enzymes, can be ligated to blunt-endedDNA fragments by T4 DNA ligase. They are subsequently digested withappropriate restriction enzymes to create cohesive ends and ligated toan expression vector with compatible termini. Adaptors are alsochemically synthesised DNA fragments which contain one blunt end usedfor ligation but which also possess one preformed cohesive end.Alternatively a DNA fragment or DNA fragments can be ligated together bythe action of DNA ligase in the presence or absence of one or moresynthetic double stranded oligonucleotides optionally containingcohesive ends.

Synthetic linkers containing a variety of restriction endonuclease sitesare commercially available from a number of sources includingSigma-Genosys Ltd, London Road, Pampisford, Cambridge, United Kingdom.

Appropriate insertion sites in plasmids (such as 2 μm-family plasmids)include, but are not limited to, those discussed above.

Host Cells

The present invention also provides a host cell comprising recombinantgenes and/or plasmid according to any aspect of the present invention.The host cell may be any type of cell. Many suitable host cellexpression systems are known, including bacteria (for example E. coliand Bacillus subtilis), yeasts (for example Saccharomyces cerevisiae,Pichia pastoris and Kluyveromyces lactis), filamentous fungi (forexample Aspergillus), plant cells, whole plants, animal cells and insectcells. Bacterial and yeast host cells may, or may not, be preferred.Bacterial host cells may be useful for cloning purposes. Yeast hostcells may be useful for expression of genes present in the plasmid.

In one embodiment the host cell may, or may not, be a yeast cell, suchas a member of the Saccharomyces, Kluyveromyces, Arxula, Yarrowia,Candida, Schizosaccharomyces, Debaryomyces, Xanthophyllomyces,Geotrichum, Ashbya, Hortaea, Schwanniomyces, Trichosporon,Xanthophyllomyces, or Pichia genus. Yeast such Saccharomyces cerevisiae,Kluyveromyces lactis, Pichia pastoris, Pichia membranaefaciens,Zygosaccharomyces rouxii, Zygosaccharomyces bailii, Zygosaccharomycesfermentati, Kluyveromyces drosphilarum, Pichia methanolica, Hansenulapolymorphs (also known as Pichia augusta), Arxula adeninivorans,Yarrowia lipolytica, Candida boidinii Candida utilis,Schizosaccharomyces pombe may, or may not, be preferred. Other suitableyeast may, or may not, include Debaryomyces hansenii, Xanthophyllomycesdendrorhous, Geotrichum candidum, Ashbya gossypii, Hortaea werneckii,Schwanniomyces occidentalis, Trichosporon domesticum, and/orXanthophyllomyces dendrorhous,

It is may, or may not, be particularly advantageous to use a yeastdeficient in one or more protein mannosyl transferases involved inO-glycosylation of proteins, for instance by disruption of the genecoding sequence, as discussed in WO 2004/083245, the contents of whichare incorporated herein by reference.

In another embodiment the host cell may, or may not, be an animal cell.For example, the animal cell may, or may not, be a mammalian cell, suchas a human cell type.

The host cell type may, or may not, be selected for compatibility with aplasmid type being used. Plasmids obtained from one yeast type can bemaintained in other yeast types (Irie et al, 1991, Gene, 108(1),139-144; Irie et al, 1991, Mol. Gen. Genet., 225(2), 257-265). Forexample, pSR1 from Zygosaccharomyces rouxii can be maintained inSaccharomyces cerevisiae. Optionally, the host cell is compatible with a2 μm-family plasmid (see above for a full description of the followingplasmids). For example, where the plasmid is based on pSR1, pSB3 or pSB4then a suitable yeast cell is Zygosaccharomyces rouxii; where theplasmid is based on pSB1 or pSB2 then a suitable yeast cell isZygosaccharomyces bailli; where the plasmid is based on pSM1 then asuitable yeast cell is Zygosaccharomyces fermentati; where the plasmidis based on pKD1 then a suitable yeast cell is Kluyveromycesdrosophilarum; where the plasmid is based on pPM1 then a suitable yeastcell is Pichia membranaefaciens; where the plasmid is based on the 2 μmplasmid then a suitable yeast cell is Saccharomyces cerevisiae orSaccharomyces carlsbergensis. It is particularly preferred that theplasmid is based on the 2 μm plasmid and the yeast cell is Saccharomycescerevisiae.

A 2 μm-family plasmid of the invention can be said to be “based on” anaturally occurring plasmid if it comprises one, two or preferably threeof the genes FLP, REP1 and REP2 having sequences derived from thatnaturally occurring plasmid.

It may, or may not, be particularly advantageous to use a yeastdeficient in one or more protein mannosyl transferases involved inO-glycosylation of proteins, for instance by disruption of the genecoding sequence.

Recombinantly expressed proteins can be subject to undesirablepost-translational modifications by the producing host cell. Forexample, the albumin protein sequence does not contain any sites forN-linked glycosylation and has not been reported to be modified, innature, by O-linked glycosylation. However, it has been found thatrecombinant human albumin (“rHA”) produced in a number of yeast speciescan be modified by O-linked glycosylation, generally involving mannose.The mannosylated albumin is able to bind to the lectin Concanavalin A.The amount of mannosylated albumin produced by the yeast can be reducedby using a yeast strain deficient in one or more of the PMT genes (WO94/04687). The most convenient way of achieving this is to create ayeast which has a defect in its genome such that a reduced level of oneof the Pmt proteins is produced. For example, there may, or may not, bea deletion, insertion or transposition in the coding sequence or theregulatory regions (or in another gene regulating the expression of oneof the PMT genes) such that little or no Pmt protein is produced.Alternatively, the yeast could be transformed to produce an anti-Pmtagent, such as an anti-Pmt antibody.

If a yeast other than S. cerevisiae is used, disruption of one or moreof the genes equivalent to the PMT genes of S. cerevisiae is alsobeneficial, e.g. in Pichia pastoris or Kluyveromyces lactis. Thesequence of PMT1 (or any other PMT gene) isolated from S. cerevisiaemay, or may not, be used for the identification or disruption of genesencoding similar enzymatic activities in other fungal species. Thecloning of the PMT1 homologue of Kluyveromyces lactis is described in WO94/04687.

The yeast may, or may not, have a deletion of the HSP150 and/or YAP3genes as taught respectively in WO 95/33833 and WO 95/23857.

A plasmid as defined above, may, or may not, be introduced into a hostthrough standard techniques. With regard to transformation ofprocaryotic host cells, see, for example, Cohen et at (1972) Proc. Natl.Acad. Sci. USA 69, 2110 and Sambrook et at (2001) Molecular Cloning, ALaboratory Manual, 3^(rd) Ed. Cold Spring Harbor Laboratory, Cold SpringHarbor, N.Y. Transformation of yeast cells is described in Sherman et at(1986) Methods In Yeast Genetics, A Laboratory Manual, Cold SpringHarbor, N.Y. The method of Beggs (1978) Nature 275, 104-109 is alsouseful. Methods for the transformation of S. cerevisiae are taughtgenerally in EP 251 744, EP 258 067 and WO 90/01063, all of which areincorporated herein by reference. With regard to vertebrate cells,reagents useful in transfecting such cells, for example calciumphosphate and DEAE-dextran or liposome formulations, are available fromStratagene Cloning Systems, or Life Technologies Inc., Gaithersburg, Md.20877, USA.

Electroporation is also useful for transforming cells and is well knownin the art for transforming yeast cell, bacterial cells and vertebratecells. Methods for transformation of yeast by electroporation aredisclosed in Becker & Guarente (1990) Methods Enzymol. 194, 182.

Generally, where a plasmid is used, it will transform not all of thehosts and it will therefore be necessary to select for transformed hostcells. Thus, a plasmid may, or may not, comprise a selectable marker,including but not limited to bacterial selectable marker and/or a yeastselectable marker. A typical bacterial selectable marker is theβ-lactamase gene although many others are known in the art. Yeastselectable marker include LEU2, TRP1, HIS3, HIS4, URA3, URA5, SFA1,ADE2, MET15, LYS5, LYS2, ILV2, FBA1, PSE1, PDI1 and PGK1. Those skilledin the art will appreciate that any gene whose chromosomal deletion orinactivation results in an inviable host, so called “essential” genes,can be used as a selective marker if a functional gene is provided onthe plasmid, as demonstrated for PGK1 in a pgk1 yeast strain (Piper andCurran, 1990, Curr. Genet. 17, 119). Suitable “essential” genes can befound within the Stanford Genome Database (SGD),http:://db.yeastgenome.org). Any “essential” gene product (e.g. aproduct of one of the PDI1, PSE1, PGK1 or FBA1 genes, and othersdescribed elsewhere in this application) which, when deleted orinactivated, does not result in an auxotrophic (biosynthetic)requirement, can be used as a selectable marker on a plasmid in a hostcell that, in the absence of the plasmid, is unable to produce that geneproduct, to achieve increased plasmid stability without the disadvantageof requiring the cell to be cultured under specific selectiveconditions. By “auxotrophic (biosynthetic) requirement” we include adeficiency which can be complemented by nutrient and other additions ormodifications to the growth medium. Cells unable to express functionalPgk1p or Fba1p can, however, be complemented by certain additions togrowth media and such gene products may not be preferred “essentialproteins” according to the present invention. Therefore, preferred“essential marker genes” in the context of the present invention arethose that, when deleted or inactivated in a host cell, result in adeficiency which cannot be complemented by any additions ormodifications to the growth medium, expect where those additions ormodifications are, for example, a polynucleotide, that can restore theability of the host cell to express the product of the “essential”marker gene, or the product of the “essential” marker gene itself.

Accordingly, a plasmid as provided by, for use in a method of, orcomprised in a host cell of, the present invention may, or may not,comprise more than one selectable marker.

One selection technique involves incorporating into the expressionvector a DNA sequence marker, with any necessary control elements, thatcodes for a selectable trait in the transformed cell. These markersinclude dihydrofolate reductase, G418 or neomycin resistance foreucaryotic cell culture, and tetracyclin, kanamycin or ampicillin (i.e.β-lactamase) resistance genes for culturing in E. coli and otherbacteria. Alternatively, the gene for such selectable trait can be onanother vector, which is used to co-transform the desired host cell.

Another method of identifying successfully transformed cells involvesgrowing the cells resulting from the introduction of the plasmid,optionally to allow the expression of a recombinant polypeptide (i.e.where a polypeptide which is encoded by a polynucleotide sequence on theplasmid and is not naturally produced by the host). Cells can beharvested and lysed and their DNA or RNA content examined for thepresence of the recombinant sequence using a method such as thatdescribed by Southern (1975) J. Mol. Biol. 98, 503 or Berent et at(1985) Biotech. 3, 208 or other methods of DNA and RNA analysis commonin the art. Alternatively, the presence of a polypeptide in thesupernatant of a culture of a transformed cell can be detected usingantibodies.

In addition to directly assaying for the presence of recombinant DNA,successful transformation can be confirmed by well known immunologicalmethods when the recombinant DNA is capable of directing the expressionof the protein. For example, cells successfully transformed with anexpression vector produce proteins displaying appropriate antigenicity.Samples of cells suspected of being transformed are harvested andassayed for the protein using suitable antibodies.

Thus, in addition to the transformed host cells themselves, the presentinvention also contemplates a culture of those cells, optionally amonoclonal (clonally homogeneous) culture, or a culture derived from amonoclonal culture, in a nutrient medium. Alternatively, transformedcells may, or may not, represent an industrially/commercially orpharmaceutically useful product and can be used without furtherpurification or can be purified from a culture medium and optionallyformulated with a carrier or diluent in a manner appropriate to theirintended industrial/commercial or pharmaceutical use, and optionallypackaged and presented in a manner suitable for that use. For example,whole cells could be immobilised; or used to spray a cell culturedirectly on to/into a process, crop or other desired target. Similarly,whole cell, such as yeast cells can be used as capsules for a hugevariety of applications, such as fragrances, flavours andpharmaceuticals.

Transformed host cells may, or may not, be cultured for a sufficienttime and under appropriate conditions known to those skilled in the art,and in view of the teachings disclosed herein, to permit the expressionof one or more recombinant chaperones and a desired protein (such as adesired heterologous protein).

The culture medium may, or may not, be non-selective or may, or may notplace a selective pressure on the maintenance of the plasmid.

The thus produced desired protein (such as a desired heterologousprotein) may, or may not, be present intracellularly or, if secreted, inthe culture medium and/or periplasmic space of the host cell.

Protein Recovery and Formulation

The step of purifying the thus expressed desired protein (such as adesired heterologous protein) from the cultured host cell or the culturemedium optionally comprises cell immobilization, cell separation and/orcell breakage, but always comprises at least one other purification stepdifferent from the step or steps of cell immobilization, separationand/or breakage.

Cell immobilization techniques, such as encasing the cells using calciumalginate bead, are well known in the art. Similarly, cell separationtechniques, such as centrifugation, filtration (e.g. cross-flowfiltration, expanded bed chromatography and the like are well known inthe art. Likewise, methods of cell breakage, including beadmilling,sonication, enzymatic exposure and the like are well known in the art.

The at least one other purification step may be any other step suitablefor protein purification known in the art. For example purificationtechniques for the recovery of recombinantly expressed albumin have beendisclosed in: WO 92/04367, removal of matrix-derived dye; EP 464 590,removal of yeast-derived colorants; EP 319 067, alkaline precipitationand subsequent application of the albumin to a lipophilic phase; and WO96/37515, U.S. Pat. No. 5,728,553 and WO 00/44772, which describecomplete purification processes; all of which are incorporated herein byreference.

Proteins other than albumin may be purified from the culture medium byany technique that has been found to be useful for purifying suchproteins.

Suitable methods include ammonium sulphate or ethanol precipitation,acid or solvent extraction, anion or cation exchange chromatography,phosphocellulose chromatography, hydrophobic interaction chromatography,affinity chromatography, hydroxylapatite chromatography, lectinchromatography, concentration, dilution, pH adjustment, diafiltration,ultrafiltration, high performance liquid chromatography (“HPLC”),reverse phase HPLC, conductivity adjustment and the like.

In one embodiment, any one or more of the above mentioned techniquesmay, or may not, be used to further purify the thus isolated protein toa commercially or industrially acceptable level of purity. Bycommercially or industrially acceptable level of purity, we include theprovision of the protein at a concentration of at least 0.01 g·L⁻¹, 0.02g·L⁻¹, 0.03 g·L⁻¹, 0.04 g·L⁻¹, 0.05 g·L⁻¹, 0.06 g·L⁻¹, 0.07 g·L⁻¹, 0.08g·L⁻¹, 0.09 g·L⁻¹, 0.1 g·L⁻¹, 0.2 g·L⁻¹, 0.3 g·L⁻¹, 0.4 g·L⁻¹, 0.5g·L⁻¹, 0.6 g·L⁻¹, 0.7 g·L⁻¹, 0.8 g·L⁻¹, 0.9 g·L⁻¹, 1 g·L⁻¹, 2 g·L⁻¹, 3g·L⁻¹, 4 g·L⁻¹, 5 g·L⁻¹, 6 g·L⁻¹, 7 g·L⁻¹, 8 g·L⁻¹, 9 g·L⁻¹, 10 g·L⁻¹,15 g·L⁻¹, 20 g·L⁻¹, 25 g·L⁻¹, 30 g·L⁻¹, 40 g·L⁻¹, 50 g·L⁻¹, 60 g·L⁻¹, 70g·L⁻¹, 70 g·L⁻¹, 90 g·L⁻¹, 100 g·L⁻¹, 150 g·L⁻¹, 200 g·L⁻¹, 250 g·L⁻¹,300 g·L⁻¹, 350 g·L⁻¹, 400 g·L⁻¹, 500 g·L⁻¹, 600 g·L⁻¹, 700 g·L⁻¹, 800g·L⁻¹, 900 g·L⁻¹, 1000 g·L⁻¹, or more.

It is preferred that the desired protein (such as a desired heterologousprotein) is purified to achieve a pharmaceutically acceptable level ofpurity. A protein has a pharmaceutically acceptable level of purity ifit is essentially pyrogen free and can be administered in apharmaceutically efficacious amount without causing medical effects notassociated with the activity of the protein.

The resulting desired protein (such as a desired heterologous protein)may, or may not, be used for any of its known utilities, which, in thecase of albumin, include i.v. administration to patients to treat severeburns, shock and blood loss, supplementing culture media, and as anexcipient in formulations of other proteins.

Although it is possible for a therapeutically, diagnostically,industrially, domestically or nutritionally useful desired protein (suchas a desired heterologous protein) obtained by a process of the of theinvention to be presented or administered alone, it is preferable topresent it as a formulation (such as a pharmaceutical formulation,particularly in the case of therapeutically and/or diagnostically usefulproteins), together with one or more acceptable carriers or diluents.The carrier(s) or diluent(s) must be “acceptable” in the sense of beingcompatible with the desired protein and, where the formulation isintended for administration to a recipient, then not deleterious to therecipient thereof. Typically, the carriers or diluents will be water orsaline which will be sterile and pyrogen free.

Optionally the thus formulated protein will be presented in a unitdosage form, such as in the form of a tablet, capsule, injectablesolution or the like.

In a sixth aspect of the present invention there is provided a methodfor producing a desired protein (such as a desired heterologousprotein), such as a desired protein as defined above for an earlieraspect of the present invention, comprising: providing a host cellcomprising a first recombinant gene encoding the protein comprising thesequence of Orm2p or a variant thereof and a second gene, optionally asecond recombinant gene, encoding a desired protein (such as a desiredheterologous protein), optionally with the proviso that the first andsecond genes are not both present within the host cell on the same 2μm-family plasmid; and culturing the host cell in a culture medium underconditions that allow the expression of the first and second genes. Themethod may, or may not, further comprise the step of purifying the thusexpressed desired protein (such as a desired heterologous protein) fromthe cultured host cell or the culture medium; and optionally,lyophilising the thus purified protein; and optionally formulating thepurified desired protein (such as a desired heterologous protein) with acarrier or diluent; and optionally presenting the thus formulatedprotein in a unit dosage form.

In the manner discussed above, the host cell may, or may not, furthercomprise a further recombinant gene encoding a protein comprising thesequence of an alternative chaperone to Orm2p or a variant thereof.

Either or both of the first and second genes in the sixth aspect of theinvention may or may not be recombinant genes that are expressed from aplasmid, and optionally from the same plasmid, provided that where bothgenes are expressed from the same plasmid then that plasmid is not a 2μm-family plasmid. A further recombinant gene encoding a proteincomprising the sequence of an alternative chaperone to Orm2p or avariant thereof may, or may not, also be expressed from a plasmid,optionally from the same plasmid as either or both of the first andsecond recombinant genes. Except where both of the first and secondgenes are recombinant genes that are co-expressed from the same plasmidthen either one may, or may not, be individually expressed from a 2μm-family plasmid, such as the 2 μm plasmid. Alternatively, one or bothof the first and second genes of the sixth aspect of the invention may,or may not, be integrated into the chromosome of the host cell. Thefurther recombinant gene encoding a protein comprising the sequence ofan alternative chaperone to Orm2p or a variant thereof may, or may not,be integrated into the chromosome of the host cell, irrespective ofwhether or not the first and second genes are expressed from a plasmidor are chromosomally integrated.

The present invention also provides, in a seventh aspect, a host cell asdefined above in respect of the sixth aspect, which host cell comprisesa first recombinant gene encoding a protein comprising the sequence ofOrm2p or a variant or fragment thereof and a second gene, such as arecombinant gene, encoding a desired protein (such as a desiredheterologous protein), optionally with the proviso that the first andsecond genes are not present within the host cell on the same 2μm-family plasmid.

The present invention also provides, in an eighth aspect, for the use ofa nucleic acid sequence encoding the protein Orm2p or a variant thereofto increase the production, in a host cell (such as a host cell asdefined above), of a desired protein (such as a desired heterologousprotein) encoded by a gene, such as a recombinant gene, in the host cellby co-expression of the nucleic acid sequence and the gene within thehost cell (but optionally not including co-expression of these genesfrom the same 2 μm-family plasmid). Either or both of the nucleic acidsequence and the gene encoding the desired protein may, or may not, beexpressed from a plasmid within the host cell, and optionally from thesame plasmid. In the manner discussed above, the host cell may, or maynot, further comprise a recombinant gene encoding an alternativechaperone to Orm2p or a variant thereof, which may, or may not, belocated on a plasmid within the host cell, optionally on the sameplasmid as either or both of the nucleic acid sequence and a geneencoding the desired protein. Suitable plasmids include a 2 μm-familyplasmid, such as the 2 μm plasmid, as discussed above.

In a ninth aspect of the present invention there is also provided theuse of a plasmid as an expression vector to increase the production of aheterologous protein by providing a recombinant gene encoding theheterologous protein and a gene encoding Orm2p or a variant thereof onthe same plasmid, optionally with the proviso that the plasmid is not a2 μm-family plasmid. The plasmid may, or may not, further comprise agene encoding an alternative chaperone to Orm2p or a variant thereof inthe manner discussed above.

Accordingly, in a tenth aspect, the present invention also provides aplasmid, optionally an expression plasmid, comprising a first geneencoding the protein Orm2p or a variant or fragment thereof and a secondgene encoding a heterologous protein, as discussed above, optionallywith the proviso that the plasmid is not a 2 μm-family plasmid. Theplasmid may, or may not, further comprise a third gene encoding analternative chaperone to Orm2p or a variant thereof. In a preferredembodiment, the third gene encodes a protein comprising the sequence ofprotein disulphide isomerase.

We have also demonstrated that a plasmid-borne gene encoding a proteincomprising the sequence of an “essential” protein can be used to stablymaintain the plasmid in a host cell that, in the absence of the plasmid,does not produce the “essential” protein. This has the advantage ofensuring the genetic stability of the organism in the chosen cultureconditions, and thereby improving the reproducibility and reliability ofindividual cultures, and furthermore enables prolonged culture withoutreduced productivity due to plasmid loss.

A preferred “essential” protein is a chaperone which may or may notprovide the further advantage that, as well as acting as a selectablemarker to increase plasmid stability, its expression simultaneouslyincreases the expression of one or more desired proteins, such as aheterologous protein encoded by a recombinant gene, within the hostcell. This system is advantageous because it allows the user to minimisethe number of recombinant genes that need to be carried by a plasmid.For example, typical prior art plasmids carry marker genes (such asthose as described above) that enable the plasmid to be stablymaintained during host cell culturing process. Such marker genes need tobe retained on the plasmid in addition to any further genes that arerequired to achieve a desired effect. However, the ability of plasmidsto incorporate exogenous DNA sequences is limited and it is thereforeadvantageous to minimise the number of sequence insertions required toachieve a desired effect. Moreover, some marker genes (such asauxotrophic marker genes) require the culturing process to be conductedunder specific conditions in order to obtain the effect of the markergene. Such specific conditions may not be optimal for cell growth orprotein production, or may require inefficient or unduly expensivegrowth systems to be used.

Thus, it is possible to use a recombinant gene that encodes a proteincomprising the sequence of an “essential” protein as a plasmid-bornegene to increase plasmid stability, where the plasmid is present withina cell that, in the absence of the plasmid, is unable to produce the“essential” protein. It will be appreciated that the question of whetheror not a protein is “essential” will depend on the system in which it isuse; it is possible that a protein that is not “essential” in one hostorganism might become “essential” when one or more other genes isdeleted, disrupted, inactivated, modified or affected in that same host,and thereby be used as an “essential” plasmid-borne gene, as describedabove; likewise whether or not a protein is “essential” may depend oncertain physical conditions, such as pH, temperature and/or oxygenlevels under which the host cell is cultured.

It is preferred that the “essential protein” is one that, when itsencoding gene(s) in a host cell are deleted or inactivated, does notresult in the host cell developing an auxotrophic (biosynthetic)requirement. By “auxotrophic (biosynthetic) requirement” we include adeficiency that can be complemented by additions or modifications to thegrowth medium, in particular additions of, or modifications to, thenutrient composition of the growth medium. Thus, the “essential protein”would be an auxotrophic marker protein if the inactivation of itsencoding gene, in a host cell, resulted in the production of anauxotrophic mutant, i.e. a mutant organism that, in order to grow andsurvive, requires a particular additional nutrient that the normal(unmutated strain) does not—it is preferred that the “essential protein”is not an auxotrophic marker protein. Therefore, an “essential markergene” which encodes an “essential protein”, in the context of thepresent invention is one that, when deleted or inactivated in a hostcell, results in a deficiency which cannot be complemented by additionsor modifications, typically nutrient additions or modifications, to thegrowth medium, expect where those additions or modifications are, forexample, a polynucleotide, that can restore the ability of the host cellto express the product of the “essential” marker gene, or the product ofthe “essential” marker gene itself. In other words, it may, or may not,be preferred if the “essential protein” is not a protein that, innature, is involved in the metabolic conversion of nutrients by a hostcell. The advantage of this system is that the “essential marker gene”can be used as a selectable marker on a plasmid in host cell that, inthe absence of the plasmid, is unable to produce that gene product, toachieve increased plasmid stability without the disadvantage ofrequiring the cell to be cultured under specific selective (e.g.selective nutrient) conditions. Therefore, the host cell can be culturedunder conditions that do not have to be adapted for any particularmarker gene, without losing plasmid stability. For example, host cellsproduced using this system can be cultured in non-selective media suchas complex or rich media, and under non-selective growth conditions(e.g. such as pH, temperature and/or oxygen levels), which may be moreeconomical, and/or more supportive growth media/conditions, than theminimal media and/or specifically adapted growth conditions that arecommonly used to give auxotrophic, and other, marker genes their effect.

The cell may, or may not, for example, have the endogenous copy (orcopies) of the gene (or genes) encoding the “essential” protein deletedor otherwise inactivated.

It is particularly preferred if the “essential protein” is an“essential” chaperone, as this can provide the dual advantage ofimproving plasmid stability without the need for selective growthconditions and increasing the production of desired proteins, such asendogenously encoded or a heterologous proteins, in the host cell. Thissystem also has the advantage that it minimises the number ofrecombinant genes that need to be carried by the plasmid if one choosesto use over-expression of an “essential” chaperone to increase proteinproduction by the host cell.

Preferred “essential proteins” for use in this aspect of the inventioninclude the “essential” chaperones encoded by the genes PDI1 and PSE1which, when the endogenous gene(s) encoding these proteins are deletedor inactivated in a host cell, do not result in the host cell developingan auxotrophic (biosynthetic) requirement.

Preferred “essential” chaperones are eucaryotic chaperones, especiallypreferred “essential” chaperones are yeast chaperones, includingchaperones comprising the sequence of proteins encoded by a geneselected from CCT2, CCT3, CCT4, CCT5, CCT6, CCT7, CCT8, CNS1, ERO1 (inthe absence of diamide), HSP10, HSP60, PDI1, CDC37, KAR2, MGE1, MRS11,NOB1, SSC1, PSE1, TIM9, PAM18 and TCP1.

It is noted that a host cell that is mutated to inactive ERO1 can becomplemented by growth in the presence of the oxidant diamide (Frand &Kaiser, 1998, Molecular Cell, 1, 161-170), but diamide is not a“nutrient” addition of the type discussed above in respect ofauxotrophic mutations. Diamide is not a commonly used component ofgrowth media and an ERO1 mutant that is transformed with a plasmidcomprising the ERO1 gene can be grown in rich media without loss ofplasmid stability.

Accordingly, in an eleventh aspect, the present invention also providesa host cell comprising a plasmid (such as a plasmid as defined above byany of the previous aspects of the invention), the plasmid comprising agene that encodes an “essential” protein, such as a chaperone, wherein,in the absence of the plasmid, the host cell is unable to produce the“essential” protein. Preferably, in the absence of the plasmid, the hostcell is inviable. Typically the host cell has been genetically modifiedto render it unable to produce a functional copy of the “essential”protein from a chromosomally-encoded (or otherwise endogenous) gene. Thehost cell may, or may not, further comprise a recombinant gene encodinga heterologous protein, such as those described above in respect ofearlier aspects of the invention.

The present invention also provides, in a twelfth aspect, a plasmidcomprising, as the sole yeast selectable marker, optionally as the soleselectable marker, a gene encoding an “essential” protein, such as an“essential” chaperone. The plasmid may, or may not, further comprise agene encoding a heterologous protein. The plasmid may, or may not, be a2 μm-family plasmid.

The present invention also provides, in a thirteenth aspect, a methodfor producing a desired protein (such as a desired heterologous protein)comprising the steps of: providing a host cell comprising a plasmid, theplasmid comprising a gene that encodes an “essential” protein, such as achaperone, wherein, in the absence of the plasmid, the host cell isunable to produce the “essential” protein and wherein the host cellfurther comprises a gene, such as a recombinant gene, encoding a desiredprotein (such as a desired heterologous protein); culturing the hostcell in a culture medium under conditions that allow the expression ofthe “essential” protein and the desired protein; and optionallypurifying the thus expressed desired protein from the cultured host cellor the culture medium; and further optionally, lyophilising the thuspurified protein. Thus, a host cell used in this method may, or may not,be a host cell according to the eleventh aspect of the invention and/orthe host call may, or may not, be transformed with a plasmid accordingto the twelfth aspect of the invention.

The method may, or may not, further comprise the step of formulating thepurified desired protein (such as a desired heterologous protein) with acarrier or diluent and optionally presenting the thus formulated proteinin a unit dosage form, in the manner discussed above.

In one preferred embodiment, the step of “culturing the host cell in aculture medium under conditions that allow the expression of the“essential” protein and the desired protein” involves culturing the hostcell in medium that is not specifically adapted to be selective for thepresence of any genes on the plasmid, other than for the presence of thegene encoding the “essential” protein. Thus, in one embodiment, the stepof culturing the host cells may, or may not, be performed innon-selective media, such as complex or rich media and/or underconditions (such as pH, temperature and/or oxygen levels) that are notspecifically adapted to select for the presence of the “essential”protein. A medium can be described as non-selective for the purposes ofthe present situation if it is not specifically adapted to deprive thehost cell of a product, typically a nutrient product, that is ordinarilyprovided to maximise, or otherwise allow, the growth of host cells thathave not been modified to prevent the expression of the “essential”protein. For example, a medium (the “test medium”) may be anon-selective medium, for the purposes of the present invention if, whenone compares plasmid stability in a first host cell type grown in the“test medium” to plasmid stability in a second cell type grown in the“test medium” when each cell type is grown for 5, 10, 15, 20, 25 or 30generations in the “test medium”, wherein—

-   (i) the first host cell type is a host cell according to the    eleventh aspect of the present invention;-   (ii) the second host cell type is a host cell according to the    eleventh aspect of the present invention except that it has been    modified to restore the ability of the host cell to produce the    “essential” protein in the absence of the plasmid (which is not to    say that the second host cell type does not contain a plasmid    encoding the “essential” protein, just that it can produce the    “essential” protein even when the plasmid is not present);    then the plasmid stability observed in the second cell type is less    than 99%, 98%, 95%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 15%,    10%, 5%, 4%, 3%, 2%, 1% or less of the plasmid stability observed in    the first cell type. Thus, in this embodiment, and despite being    grown under non-selective conditions, it is preferable for method of    the thirteenth aspect of the present invention to produce host cells    which display substantially 100% plasmid stability after 5, 10, 15,    20, 25 or 30 generations.

A fourteenth aspect of the present invention also provides for the useof a polynucleotide that encodes an “essential” protein (as definedabove) to increase the stability of a plasmid in a host cell,particularly under non-selective conditions, by integration of thepolynucleotide into the plasmid to produce a modified plasmid, whereinthe host cell is unable to produce the “essential” protein in theabsence of the modified plasmid. The increase in stability may, or maynot, be at least 1% (i.e. 1.01 times), 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%,10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% (i.e. 2-fold), 3-fold,4-fold, 5-fold, 6-fold s, 7-fold, 8-fold, 9-fold, 10-fold or moregreater than the level of stability of the unmodified plasmid in thesame host cell that has been modified to produce the “essential”protein, when grown for at least five generations under non-selectiveconditions.

In one embodiment of the fourteenth aspect of the present invention, theplasmid may, or may not, additionally comprise a gene that encodes afurther desired heterologous protein, such as defined above in respectof earlier aspects of the present invention. In that case, the use may,or may not, be to improve the productivity of the desired heterologousprotein, such as when the host cell comprising the plasmid is grownunder non-selective conditions.

In one preferred embodiment, the “essential” protein is a chaperone andmay, or may not, be used to simultaneously increase the stability of aplasmid in the host cell and increase the ability of the host cell toproduce a desired protein product. The desired protein product may, ormay not, be an endogenously encoded protein or may, or may not, be aheterologous protein as defined by the earlier aspects of the invention.Where the protein product is a heterologous protein, it may, or may not,be encoded by a recombinant gene that has been integrated into thechromosome of the host cell, or by a gene that is present on a plasmidin the host cell, such as the modified plasmid comprising thepolynucleotide that encodes the “essential” protein as defined above.

We have also found that the effects of recombinantly-provided chaperonesaccording to the other embodiments of the present invention can bemodulated by modifying the promoters that control the expression levelsof the chaperone(s). Surprisingly we have found that, in some cases,shorter promoters result in increased expression of a desired protein.Without being bound by theory we believe that this is because theexpression of a recombinant chaperone in host cells that already expressdesired proteins at high levels can cause the cells to overloadthemselves with desired protein (such as a desired heterologousprotein), thereby achieving little or no overall increase in productionof the desired protein. In those cases, it may, or may not, bebeneficial to provide recombinant chaperone genes with truncatedpromoters.

Accordingly, in a fifteenth aspect of the present invention there isprovided a polynucleotide (such as a plasmid as defined above)comprising the sequence of a promoter operably connected to a codingsequence encoding a chaperone (such as those described above), for usein increasing the expression of a desired protein (such as a desiredheterologous protein), such as those described above, in a host cell(such as those described above) by expression of the polynucleotidesequence within the host cell, wherein the promoter is characterised inthat it achieves a modified, such as a higher or lower, level ofexpression of the chaperone than would be achieved if the codingsequence were to be operably connected to its naturally occurringpromoter.

The present invention also provides, in a sixteenth aspect, a method forproducing a desired protein (such as a desired heterologous protein)comprising the steps of: providing a host cell comprising a recombinantgene that comprising the sequence of promoter operably connected to acoding sequence encoding a chaperone, the promoter being characterisedin that it achieves a lower level of expression of the chaperone thanwould be achieved if the coding sequence were to be operably connectedto its naturally occurring promoter, and the host cell furthercomprising a gene, such as a recombinant gene, encoding a desiredprotein (such as a desired heterologous protein); culturing the hostcell under conditions that allow the expression of the chaperone and thedesired protein; and optionally purifying the thus expressed desiredprotein from the cultured host cell or the culture medium; and furtheroptionally, lyophilising the thus purified protein; and optionallyfurther formulating the purified desired protein with a carrier ordiluent; and optionally presenting the thus formulated protein in a unitdosage form, in the manner discussed above.

As is apparent from the examples of the present application, thecombination of recombinantly expressed PDI and transferrin-basedproteins provides a surprisingly high level of transferrin expression.For example, transferrin expression in a system that includes achromosomally encoded recombinant PDI gene provided a 2-fold increase(compared to a control in which there is no chromosomally encodedrecombinant PDI gene). This increase was 5-times greater than anequivalent system comprising a recombinant gene encoding human albuminin place of the recombinant transferrin gene.

The host may be any cell type, such as a procaryotic cell (e.g.bacterial cells such as E. coli) or a eucaryotic cell. Preferredeucaryotic cells include fungal cells, such as yeast cells, andmammalian cells. Exemplary yeast cells are discussed above. Exemplarymammalian cells include human cells.

Host cells as described above can be cultured to produce recombinanttransferrin-based proteins. The thus produced transferrin-based proteinscan be isolated from the culture and purified, optionally to apharmaceutically acceptable level of purity, for example usingtechniques known in the art and/or as set out above. Purifiedtransferrin-based proteins may, or may not, be formulated with apharmaceutically acceptable carrier or diluent and may, or may not, bepresented in unit dosage form.

The present invention will now be exemplified with reference to thefollowing non-limiting examples and figures.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a map of a typical 2 μm plasmid.

FIG. 2 shows the results of rocket immunoelectrophoresis (RIE)determination of increased recombinant transferrin (N413Q, N611Q)secretion with PDI1 over-expression. Cryopreserved yeast stocks weregrown for 4-days in 10 mL BMMD shake flask cultures and supernatantswere loaded at 54 per well. Goat polyclonal anti-transferrin (human)antiserum (Calbiochem) was used at 404 per rocket immunoelectrophoresisgel (50 mL). A=Control strain [pSAC35], duplicate flasks; B=Controlstrain [pDB2536], duplicate flasks; C=Control strain [pDB2711], neat to40-fold aqueous dilutions; D=Control strain [pDB2931], duplicate flasks;E=Control strain [pDB2929], neat to 40-fold aqueous dilutions.

FIG. 3 shows the results of RIE analysis of recombinant transferrin(N413Q, N611 Q) secretion with and without PDI1 over-expression.Cryopreserved yeast stocks were grown for 4-days in 10 mL BMMD shakeflask cultures and supernatants were loaded at 5 μL per well. Duplicateloadings were made of supernatants from two individual cultures of eachstrain. Goat polyclonal anti-transferrin (human) antiserum (Calbiochem)was used at 40 μL per rocket immunoelectrophoresis gel (50 mL).A=Control strain [pSAC35]; B=Control strain [pDB2536]; C=Control strain[pDB2711]; D=Control strain [pDB2931]; E=Control strain [pDB2929].

FIG. 4 shows the results of SDS-PAGE analysis of recombinant transferrinsecretion with and without PDI1 over-expression. BMMD shake flaskcultures were grown for 4-days and 10 μL supernatant analysed onnon-reducing SDS-PAGE (4-12% NuPAGE®, MOPS buffer, InVitrogen) withGelCode® Blue reagent (Pierce). 1=SeeBlue Plus2 Markers (InVitrogen).2=pDB2536; 3=pDB2536; 4=pDB2711; 5=pDB2711; 6=pDB2931; 7=pDB2931;8=pDB2929; 9=pDB2929; 10=pSAC35 control.

FIG. 5 shows RIE analysis of recombinant transferrin secretion from S.cerevisiae strains with an additional integrated copy of PDI1. 5-dayBMMD shake flask culture supernatants were loaded at 5 mL per well.Strains contained: 1) pSAC35 (negative control); 2) pDB2536 (recombinantnon-glycosylated transferrin (N413Q, N611Q)) or 3) pDB2506 (same asplasmid pDB2536 but the transferrin ORF encodes transferrin without theN→Q mutations at positions 413 and 611, i.e. recombinant glycosylatedtransferrin). Each well contained a sample derived from an individualtransformant. Standards were human plasma holo-transferrin (Calbiochem)at 100, 50, 20, 10, 5 and 2 mg·L⁻¹.

FIG. 6 shows RIE analysis of recombinant transferrin secretion fromStrain A [pDB2536] and Strain A [pDB2506] grown in shake flask culture.5-day BMMD or YEPD shake flask culture supernatants were loaded induplicate at 5 mL per well.

FIG. 7 shows SDS-PAGE analysis of recombinant transferrin secreted fromStrain A [pDB2536] and Strain A [pDB2506] grown in shake flask culture.Cultures were grown for 5-days in BMMD and 30 mL supernatants analysedon SDS-PAGE (4-12% NuPAGE™, MOPS Buffer, InVitrogen) stained withGelCode, Blue Reagent (Pierce). 1) Strain A [pDB2536] transformant 1; 2)Strain A [pDB2536] transformant 2; 3) Strain A [pSAC35] control; 4)Strain A [pDB2506] transformant 1; 5) SeeBlue, Plus2 Protein Standards(approximate molecular weights only).

FIG. 8 shows RIE of recombinant transferrin secreted from S. cerevisiaestrains with different PDI1 copy numbers. 3-day BMMD shake flask culturesupernatants were loaded at 5 mL per well. Goat polyclonalanti-transferrin (human) antiserum (Calbiochem) was used at 30 mL perrocket immunoelectrophoresis gel (50 mL). (A) supernatant from S.cerevisiae control strain [pDB2711] or [pDB2712]; (B) supernatant fromStrain A [pDB2536]; (C) supernatant from control strain [pDB2536].

FIG. 9 shows SDS-PAGE analysis of recombinant transferrin secreted fromS. cerevisiae strains with different PDI1 copy numbers. 4-12% NuPAGEreducing gel run with MOPS buffer (InVitrogen) after loading with 30 mLof 3-day BMMD shake flask culture supernatant per lane; (lane 1)supernatant from control strain [pDB2536]; (lane 2) supernatant fromStrain A [pDB2536]; (lanes 3-6) supernatant from control strain[pDB2711] or [pDB2712]; (lane 7) molecular weight markers (SeeBluePlus2, InVitrogen).

FIG. 10 shows RIE of recombinant transferrin secreted from different S.cerevisiae strains with and without additional PDI1 gene co-expression.10 mL YEPD shake flasks were inoculated with yeast and incubated for4-days at 30° C. 5 μL, culture supernatant loaded per well of a rocketimmunoelectrophoresis gel. Plasma Tf standards concentrations are inμg/mL. 20 μL goat anti-Tf/50 mL agragose. Precipin was stained withCoomassie blue.

FIG. 11 shows RIE analysis of rHA expression in different S. cerevisiaestrains when co-expressed with PDI1 genes having different lengthpromoters. 10 mL YEPD shake flasks were inoculated with yeast andincubated for 4-days at 30° C. 4 μL culture supernatant loaded per wellof a rocket immunoelectrophoresis gel. rHA standards concentrations arein μg/mL. 4004 goat anti-HA (Sigma product A-1151 resuspended in 5 mLwater)/50 mL agarose. Precipin was stained with Coomassie blue.

FIG. 12 shows RIE analysis of rHA expression in different S. cerevisiaestrains when co-expressed with PDI1 genes having different lengthpromoters. 10 mL YEPD shake flasks were inoculated with yeast andincubated for 4-days at 30° C. 4 μL culture supernatant loaded per wellof a rocket immunoelectrophoresis gel. rHA standards concentrations arein μg/mL. 400 μL goat anti-HA (Sigma product A-1151 resuspended in 5 mLwater)/50 mL agarose. Precipin was stained with Coomassie blue.

FIG. 13 shows RIE analysis of rHA fusion proteins with and withoutco-expressed recombinant PDI1. 10 mL BMMD shake flasks were inoculatedwith YBX7 transformed with albumin fusion expression plasmids andincubated for 4-days at 30° C. 4 μL culture supernatant loaded per wellof a rocket immunoelectrophoresis gel. rHA standards concentrations arein μg/mL. 2004 goat anti-HA (Sigma product A-1151 resuspended in 5 mLwater)/50 mL agarose. Precipin was stained with Coomassie blue.

FIG. 14 shows SDS-PAGE analysis of recombinant albumin fusion secretionwith and without PDI1 present on the expression plasmid. 10 mL BMMDshake flasks were inoculated with yeast and incubated for 4-days at 30°C., 200 rpm. 30 μL supernatant analysed on non-reducing SDS-PAGE (4-12%NuPAGE®, MES buffer, InVitrogen) with GelCode® Blue reagent (Pierce).1=SeeBlue Plus2 Markers (InVitrogen); 2=1 μg rHA; 3=angiostatin-rHA;4=angiostatin-rHA+PDI1; 5=endostatin-rHA; 6=endostatin-rHA+PDI1;7=DX-890-(GGS)₄GG-rHA; 8=DX-890-(GGS)₄GG-rHA+PDI1;9=DPI-14-(GGS)₄GG-rHA; 10=DPI-14-(GGS)₄GG-rHA+PDI1; 11=Axokine™(CNTF_(Ax15))-(GGS)₄GG-rHA (Lambert et al, 2001, Proc. Natl. Acad. Sci.USA, 98, 4652-4657); 12=Axokine™ (CNTF_(Ax15))-(GGS)₄GG-rHA+PDI1.

FIG. 15 shows RIE analysis demonstrating increased transferrin secretionfrom S. cerevisiae with ORM2 co-expression from a 2 μm-based plasmid.Four day shake flask culture supernantants were loaded at 5 μl per well.Standards were human plasma holo-transferrin (Calbiochem), at 25, 20,15, 10, 5 μg/ml, loaded 5 μl per well. Goat polyclonal anti-transferrin(human) antiserum (Calbiochem) used at 20 μl per rocketimmunoelectrophoresis gel (50 ml).

FIG. 16 shows RIE analysis demonstrating increased transferrin secretionfrom S. cerevisiae with PSE1 co-expression from a 2 μm-based plasmid.Four day shake flask culture supernantants were loaded at 5 μl per well.Standards were human plasma holo-transferrin (Calbiochem), at 25, 20,15, 10, 5 μg/ml, loaded 5 μl per well. Goat polyclonal anti-transferrin(human) antiserum (Calbiochem) used at 20 μl per rocketimmunoelectrophoresis gel (50 ml).

FIG. 17 shows RIE analysis demonstrating increased transferrin secretionfrom S. cerevisiae with SSA1 co-expression from a 2 μm-based plasmid.Four day shake flask culture supernantants were loaded at 5 μl per well.Standards were human plasma holo-transferrin (Calbiochem), at 25, 20,15, 10, 5 μg/ml, loaded 5 μl per well. Goat polyclonal anti-transferrin(human) antiserum (Calbiochem) used at 20 μl per rocketimmunoelectrophoresis gel (50 ml).

FIG. 18 shows the results of RIE. 10 mL YEPD shake flasks wereinoculated with DXY1 trp1Δ [pDB2976], DXY1 trp1Δ [pDB2977], DXY1 trp1Δ[pDB2978], DXY1 trp1Δ [pDB2979], DXY1 trp1Δ [pDB2980] or DXY1 trp1Δ[pDB2981] transformed to tryptophan prototrophy with a 1.41 kb NotI/PstIpdi1::TRP1 disrupting DNA fragment was isolated from pDB3078.Transformants were grown for 4-days at 30° C., 200 rpm. 4 μL culturesupernatant loaded per well of a rocket immunoelectrophoresis gel. rHAstandards concentrations are in μg/mL. 700 μL goat anti-HA (Sigmaproduct A-1151 resuspended in 5 mL water)/50 mL agarose. Precipin wasstained with Coomassie blue. Isolates selected for further analysis areindicated (*).

FIG. 19 shows the results of RIE. 10 mL YEPD shake flasks wereinoculated with DXY1 [pDB2244], DXY1 [pDB2976], DXY1 trp1Δ pdi1::TRP1[pDB2976], DXY1 [pDB2978], DXY1 trp1Δ pdi1::TRP1 [pDB2978], DXY1[pDB2980], DXY1 trp1Δ pdi1::TRP1 [pDB2980], DXY1 [pDB2977], DXY1 trp1Δpdi1::TRP1 [pDB2977], DXY1 [pDB2979] DXY1 trp1Δ pdi1::TRP1 [pDB2979],DXY1 [pDB2981] and DXY1 trp1Δ pdi1::TRP1 [pDB2981], and were grown for4-days at 30° C., 200 rpm. 4 μL culture supernatant loaded per well of arocket immunoelectrophoresis gel. rHA standards concentrations are inμg/mL. 8004 goat anti-HA (Sigma product A-1151 resuspended in 5 mLwater)/50 mL agarose. Precipin was stained with Coomassie blue. Isolatesselected for further analysis are indicated (*)

FIGS. 20A, 20B and 20C show a sequence alignment of the SKQ2n (SEQ IDNO:47) and S288c (SEQ ID NO:46) gene sequences with long promoters, asdescribed in Example 6.

FIGS. 21 to 33 show various plasmid maps.

FIG. 34 shows Rocket Immunoelectrophoresis of YEPD shake flask culturesupernatants from DXY1 and DXY1 Δtrp1 pdi1::TRP1 containing pDB3175 topDB3178. 10 mL YEPD shake flasks were inoculated with DXY1 [pAYE316],DXY1 [pDB3175], DXY1 [pDB3176], DXY1 [pDB3177], DXY1 [pDB3178], DXY1Δtrp1 pdi1::TRP1 [pDB3175], DXY1 Δtrp1 pdi1::TRP1 [pDB3176], DXY1 Δtrp1pdi1::TRP1 [pDB3177], and DXY1 Δtrp1 pdi1::TRP1 [pDB3178] were grown for4-days at 30° C., 200 rpm. 54 culture supernatant was loaded per well ofa 50 mL rocket immunoelectrophoresis gel in triplicate. rHA standardconcentrations were 300, 200, 150, 100 and 50 μg/mL. 6004 goat anti-HSA(Sigma product A-1151 resuspended in 5 mL water) per 50 mL agarose gel.Precipitin was stained with Coomassie blue.

FIG. 35 shows Rocket Immunoelectrophoresis of YEPD shake flask culturesupernatants from DXY1 and DXY1 Δtrp1 pdi1::TRP1 containing pDB3179 topDB3182. 10 mL YEPD shake flasks were inoculated with DXY1 [pDB2931],DXY1 [pDB3179], DXY1 [pDB3180], DXY1 [pDB3181], DXY1 [pDB3182], DXY1Δtrp1 pdi1::TRP1 [pDB3179], DXY1 Δtrp1 pdi1::TRP1 [pDB3180], DXY1 Δtrp1pdi1::TRP1 [pDB3181], and DXY1 Δtrp1 pdi1::TRP1 [pDB3182] were grown for4-days at 30° C., 200 rpm. 54 culture supernatant was loaded per well ofa 50 mL rocket immunoelectrophoresis gel in triplicate. Plasmatransferrin standard concentrations were 100, 50, 20, 10 and 5 μg/mL.404 goat polyclonal anti human transferrin antiserum (Calbiochem) wasused per 50 mL agarose gel. Precipitin was stained with Coomassie blue.

EXAMPLES

Two types of expression cassette have been used to exemplify secretionof a recombinant human transferrin mutant (N413Q, N611 Q) from S.cerevisiae. One type uses a modified HSA(pre)/MFα1 (pro) leader sequence(named the “modified fusion leader” sequence). The second type ofexpression cassette uses only the modified HSA(pre) leader sequence.

The 24 amino acid sequence of the “modified fusion leader” is

MKWVFIVSILFLFSSAYSRSLDKR.

The 18 amino acid sequence of the modified HSA(pre) leader sequence is

MKWVFIVSILFLFSSAYS.

Transferrin (N413Q, N611Q) expression using these two cassettes has beenstudied in S. cerevisiae using the 2 μm expression vector with andwithout an additional copy of the S. cerevisiae PDI gene, PDI1.

Example 1 Construction of Expression Plasmids

Plasmids pDB2515, pDB2529, pDB2536, pDB2688, pDB2690, pDB2711, pDB2921,pDB2928, pDB2929, pDB2930, pDB2931, pDB2932 and pDB2690 were constructedas described in Example 1 of WO 2005/061718, the contents of which areincorporated herein by reference.

Example 2 Expression of Transferrin

A S. cerevisiae control strain was transformed to leucine prototrophywith all the transferrin (N413Q, N611Q) expression plasmids, andcryopreserved stocks were prepared.

Strains were grown for four days at 30° C. in 10 mL BMMD cultures in 50mL conical flasks shaken at 200 rpm. The titres of recombinanttransferrin secreted into the culture supernatants were compared byrocket immunoelectrophoresis (RIE as described in Weeke, B., 1976,“Rocket immunoelectrophoresis” In N. H. Azelsen, J. Kroll, and B. Weeke[eds.], A manual of quantitative immunoelectrophoresis. Methods andapplications. Universitetsforlaget, Oslo, Norway), reverse phase highperformance liquid chromatography (RP-HPLC) (Table 1), and non-reducingSDS polyacrylamide electrophoresis stained with colloidal Coomassie bluestain (SDS-PAGE). The increase in recombinant transferrin secreted whenS. cerevisiae PDI1 was over-expressed was estimated to be greater than10-fold.

By RP-HPLC analysis (using the method described in Example 2 of WO2005/061718, the contents of which are incorporated herein by reference)the increase in transferrin secretion was determined to be 18-fold forthe modified fusion leader sequence and 15-fold for the modified HSA-preleader sequence (Table 1).

FIG. 4 shows an SDS-PAGE comparison of the recombinant transferrinsecreted by S. cerevisiae strains with and without additional PDI1expression.

TABLE 1 Average Transferrin Titre Estimated Secretory Additional (μg ·mL⁻¹) Increase due to Plasmid Leader PDI1 (n = 2) Additional PDI1 pSAC35None No 0.4 — pDB2536 Fusion No 6.2 — Leader pDB2711 Fusion Yes 112.818-fold Leader pDB2931 Modified No 5.1 — HSA-pre Leader pDB2929 ModifiedYes 76.1 15-fold HSA-pre Leader

RIE analysis indicated that the increased transferrin secretion in thepresence of additional copies of PDI1 was approximately 15-fold (FIG.2). By RIE analysis the increase appeared slightly larger for themodified HSA-pre leader sequence than for the modified fusion leadersequence (FIG. 3).

Example 3 Chromosomal Over-Expression of PDI

S. cerevisiae Strain A was selected to investigate the secretion ofrecombinant glycosylated transferrin expression from plasmid pDB2506 andrecombinant non-glycosylated transferrin (N413Q, N611Q) from plasmidpDB2536. Strain A has the following characteristics—

-   -   additional chromosomally integrated PDI1 gene integrated at the        host PDI1 chromosomal location.    -   the URA3 gene and bacterial DNA sequences containing the        ampicillin resistance gene were also integrated into the S.        cerevisiae genome at the insertion sites for the above genes.

A control strain had none of the above insertions.

Control strain [cir⁰] and Strain A [cir⁰] were transformed to leucineprototrophy with pDB2506 (recombinant transferrin), pDB2536 (recombinantnon-glycosylated transferrin (N413Q, N611Q)) or pSAC35 (control).Transformants were selected on BMMD-agar.

The relative level of transferrin secretion in BMMD shake flask culturewas determined for each strain/plasmid combination by rocketimmunoelectrophoresis (RIE). FIG. 5 shows that both strains secretedboth the glycosylated and non-glycosylated recombinant transferrins intothe culture supernatant.

The levels of both the glycosylated and non-glycosylated transferrinssecreted from Strain A [pDB2506] and Strain A [pDB2536] respectively,appeared higher than the levels secreted from the control strain. Hence,at least in shake flask culture, PDI1 integrated into the host genome atthe PDI1 locus in Strain A has enhanced transferrin secretion.

Furthermore, the increase in transferrin secretion observed betweencontrol strain [pDB2536] and Strain A [pDB2536] appeared to be at leasta 100% increase by RIE. In contrast, the increase in rHA monomersecretion between control strain [pDB2305] and Strain A [pDB2305] wasapproximately 20% (data not shown). Therefore, the increase intransferrin secretion due to the additional copy of PDI1 in Strain A wassurprising large considering that transferrin has 19 disulphide bonds,compared to rHA with 17 disulphide bonds. Additional copies of the PDI1gene may be particularly beneficial for the secretion from S. cerevisiaeof proteins from the transferrin family, and their derivatives.

The levels of transferrin secreted from Strain A [pDB2536] and Strain A[pDB2506] were compared by RIE for transformants grown in BMMD and YEPD(FIG. 6). Results indicated that a greater than 2-fold increase intitres of both non-glycosylated recombinant transferrin (N413Q, N611Q)and glycosylated recombinant transferrin was achieved by growth in YEPD(10-20 mg·L⁻¹ serum transferrin equivalent) compared to BMMD (2-5 mg·L⁻¹serum transferrin equivalent). The increase in both glycosylated andnon-glycosylated transferrin titre observed in YEPD suggested that bothtransferrin expression plasmids were sufficiently stable undernon-selective growth conditions to allow the expected increased biomasswhich usually results from growth in YEPD to be translated intoincreased glycosylated and non-glycosylated transferrin productivity.

SDS-PAGE analysis of non-glycosylated transferrin (N413Q, N611Q)secreted from Strain A [pDB2536] and glycosylated transferrin fromStrain A [pDB2506] grown in BMMD shake flask culture is shown in FIG. 7.Strain A [pDB2536] samples clearly showed an additional protein bandcompared to the Strain A [pSAC35] control. This extra band migrated atthe expected position for the recombinant transferrin (N413Q, N611Q)secreted from control strain [pDB2536]. Strain A [pDB2506] culturesupernatants appeared to contain a diffuse protein band at the positionexpected for transferrin. This suggested that the secreted recombinanttransferrin was heterogeneous, possibly due to hyper-mannosylation atAsp413 and/or Asp611.

Example 4 Comparing Transferrin Secretion from S. cerevisiae ControlStrain Containing pDB2711 with Transferrin Secretion from S. cerevisiaeStrain A

Plasmid pDB2711 is as described above. Plasmid pDB2712 (FIG. 22 of WO2005/061718) was also produced with the NotI cassette in the oppositedirection to pDB2711.

Control strain S. cerevisiae [cir⁰] was transformed to leucineprototrophy with pDB2711 and pDB2712. Transformants were selected onBMMD-agar and cryopreserved trehalose stocks of control strain [pDB2711]were prepared. Secretion of recombinant transferrin (N413Q, N611Q) bycontrol strain [pDB2711], control strain [pDB2712], Strain A [pDB2536],control strain [pDB2536] and an alternative control strain [pDB2536] wascompared in both BMMD and YEPD shake flask culture. RIE indicated that asignificant increase in recombinant transferrin secretion had beenachieved from control strain [pDB2711] with multiple episomal PDI1copies, compared to Strain A [pDB2536] with two chromosomal copies ofPDI1, and control strain [pDB2536] with a single chromosomal copy ofPDI1 gene (FIG. 8). Control strain [pDB2711] and control strain[pDB2712] appeared to secrete similar levels of rTf (N413Q, N611 Q) intothe culture media. The levels of secretion were relatively consistentbetween control strain [pDB2711] and control strain [pDB2712]transformants in both BMMD and YEPD media, suggesting that plasmidstability was sufficient for high-level transferrin secretion even undernon-selective conditions. This is in contrast to the previous publisheddata in relation to recombinant PDGF-BB and HSA where introduction ofPDI1 into multicopy 2 μm plasmids was shown to be detrimental to thehost.

TABLE 2 Recombinant transferrin titres from high cell densityfermentations Supernatant (g · L⁻¹) Strain GP-HPLC SDS-PAGE Control[pDB2536] 0.5/0.4 — Alternative control [pDB2536] 1.5/1.6 0.6 0.9/0.90.4/0.4/0.5 Strain A [pDB2536] 0.7 0.6 0.6 — Control [pDB2711] 3.5 3.63.4 2.7/3.1

Reducing SDS-PAGE analysis of transferrin secreted from control strain[pDB2711], control strain [pDB2712], Strain A [pDB2536], control strain[pDB2536] and alternative control strain [pDB2536] in BMMD shake flaskculture is shown in FIG. 9. This shows an abundant protein band in allsamples from control strain [pDB2711] and control strain [pDB2712] atthe position expected for transferrin (N413Q, N611Q). The relative stainintensity of the transferrin (N413Q, N611Q) band from the differentstrains suggested that Strain A [pDB2536] produced more than controlstrain [pDB2536] and alternative control strain [pDB2536], but thatthere was an even more dramatic increase in secretion from controlstrain [pDB2711] and control strain [pDB2712]. The increased recombinanttransferrin secretion observed was concomitant with the increased PDI1copy number in these strains. This suggested that Pdi1p levels werelimiting transferrin secretion in control strain, Strain A and thealternative control strain, and that elevated PDI1 copy number wasresponsible for increased transferrin secretion. Elevated PDI1 copynumber could increase the steady state expression level of PDI1 soincreasing the amount of Pdi1p activity. There are a number ofalternative methods by which this could be achieved without increasingthe copy number of the PDI1 gene, for example the steady state PDI1 mRNAlevel could be increased by either increasing the transcription rate,say by use of a higher efficiency promoter, or by reducing the clearancerate of the PDI1 mRNA. Alternatively, protein engineering could be usedto enhance the specific activity or turnover number of the Pdi1pprotein.

In high cell density fermentations control strain [pDB2711] recombinanttransferrin (N413Q, N611Q) production was measured at approximately 3g·L⁻¹ by both GP-HPLC analysis and SDS-PAGE analysis (Table 2). Thislevel of production is several fold-higher than control strain, thealternative control strain or Strain A containing pDB2536. Furthermore,for the production of proteins for therapeutic use in humans, expressionsystems such as control strain [pDB2711] have advantages over thoseusing Strain A, as they do not contain bacterial DNA sequences.

CONCLUSIONS

Secretion of recombinant transferrin from a multicopy expression plasmid(pDB2536) was investigated in S. cerevisiae strains containing anadditional copy of the PDI1 gene integrated into the yeast genome.Transferrin secretion was also investigated in S. cerevisiae transformedwith a multicopy expression plasmid, in which the PDI1 gene has beeninserted into the multicopy episomal transferrin expression plasmid(pDB2711).

A S. cerevisiae strain with an additional copy of the PDI1 geneintegrated into the genome at the endogenous PDI1 locus, secretedrecombinant transferrin and non-glycosylated recombinant transferrin(N413Q, N611Q) at an elevated level compared to strains containing asingle copy of PDI1. A further increase in PDI1 copy number was achievedby using pDB2711 In high cell density fermentation of the straintransformed with pDB2711, recombinant transferrin (N413Q, N611Q) wassecreted at approximately 3 g·L⁻¹, as measured by SDS-PAGE and GP-HPLCanalysis. Therefore, increased PDI1 gene copy number has produced alarge increase in the quantity of recombinant transferrins secreted fromS. cerevisiae.

The following conclusions are drawn—

1. In shake flask analysis of recombinant transferrin expression frompDB2536 (non-glycosylated transferrin (N413Q, N611Q) and pDB2506(glycosylated transferrin) the S. cerevisiae strain Strain A secretedhigher levels of both recombinant transferrins into the culturesupernatant than control strains. This was attributed to the extra copyof PDH integrated at the PDI1 locus.

2. Control strain [pDB2711], which contained the PDI1 gene on themulticopy expression plasmid, produced a several-fold increase inrecombinant transferrin (N413Q, N611Q) secretion compared to Strain A[pDB2536] in both shake flask culture and high cell densityfermentation.

3. Elevated PDI1 copy number in yeast such as S. cerevisiae will beadvantageous during the production of desired proteins (such as adesired heterologous proteins), such as those from the transferrinfamily.

4. pSAC35-based plasmids containing additional copies of PDI1 gene haveadvantages for the production of proteins from the transferrin family,and their derivatives, such as fusions, mutants, domains and truncatedforms.

Example 5 Insertion of a PDH Gene into a 2 μm-Like Plasmid IncreasedSecretion of Recombinant Transferrin from Various Different S.cerevisiae Strains

The S. cerevisiae strain JRY188 cir⁺ (National Collection of YeastCultures) and MT302/28B cir⁺ (Finns et al., 1993, Eur. J. Biochem., 212,201-210) was cured of the native 2 μm plasmid by galactose inducedover-expression of FLP from Yep351-GAL-FLP1, as described by Rose andBroach (1990, Meth. Enzymol., 185, 234-279) to create the S. cerevisiaestrains JRY188 cir⁰ and MT302/28B cir⁰, respectively.

The S. cerevisiae strains JRY188 cir⁰, MT302/28B cir⁰, 5150-2B cir⁰(Cashmore et al., 1986, Mol. Gen. Genet., 203, 154-162), CB11-63 cir⁰(Zealey et al., 1988, Mol. Gen. Genet., 211, 155-159) were alltransformed to leucine prototrophy with pDB2931 (FIG. 14 of WO2005/061718) and pDB2929 (FIG. 12 of WO 2005/061718). Transformants wereselected on appropriately supplemented minimal media lacking leucine.Transformants of each strain were inoculated into 10 mL YEPD in 50 mLshake flasks and incubated in an orbital shaker at 30° C., 200 rpm for4-days. Culture supernatants were harvested and the recombinanttransferrin titres compared by rocket immunoelectrophoresis (FIG. 10).The results indicated that the transferrin titres in supernatants fromall the yeast strains were higher when PDI1 was present in the 2 μmplasmid (pDB2929) than when it was not (pDB2931)

Example 6 The Construction of Expression Vectors Containing Various PDI1Genes and the Expression Cassettes for Various Heterologous Proteins onthe Same 2 μm-Like Plasmid

PCR Amplification and Cloning of PDI1 Genes into YIplac211:

The PDI1 genes from S. cerevisiae S288c and S. cerevisiae SKQ2n wereamplified by PCR to produce DNA fragments with different lengths of the5′-untranslated region containing the promoter sequence. PCR primerswere designed to permit cloning of the PCR products into the EcoRI andBamHI sites of YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534).Additional restriction endonuclease sites were also incorporated intoPCR primers to facilitate subsequent cloning. Table 3 describes theplasmids constructed and Table 4 gives the PCR primer sequences used toamplify the PDI1 genes. Differences in the PDI1 promoter length withinthese YIplac211-based plasmids are described in Table 3.

pDB2939 (FIG. 27 of WO 2005/061718) was produced by PCR amplification ofthe PDI1 gene from S. cerevisiae S288c genomic DNA with oligonucleotideprimers DS248 and DS250 (Table 5), followed by digesting the PCR productwith EcoRI and BamHI and cloning the approximately 1.98-kb fragment intoYIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534), that had been cutwith EcoRI and BamHI. DNA sequencing of pDB2939 identified a missing ‘G’from within the DS248 sequence, which is marked in bold in Table 4.Oligonucleotide primers used for sequencing the PDI1 gene are listed inTable 5, and were designed from the published S288c PDI1 gene sequence(PDI1/YCL043C on chromosome III from coordinates 50221 to 48653 plus1000 base pairs of upstream sequence and 1000 base pairs of downstreamsequence. (http://www.yeastgenome.org/ Genebank Accession numberNC001135).

TABLE 3 YIplac211-based Plasmids Containing PDI1 Genes Plasmid PDI1 GenePlasmid Base Source Promoter Terminator PCR Primers pDB2939 YIplac211S288c Long (~210-bp) → Bsu36I DS248 + DS250 pDB2941 YIplac211 S288cMedium (~140-bp) → Bsu36I DS251 + DS250 pDB2942 YIplac211 S288c Short(~80-bp) → Bsu36I DS252 + DS250 pDB2943 YIplac211 SKQ2n Long (~210-bp) →Bsu36I DS248 + DS250 pDB2963 YIplac211 SKQ2n Medium (~140-bp) → Bsu36IDS267 + DS250 pDB2945 YIplac211 SKQ2n Short (~80-bp) → Bsu36I DS252 +DS250

TABLE 4 Oligonucleotide Primers for PCR  Amplification of S. cerevisiaePDI1 Genes Primer Sequence DS248 5′-GTCAGAATTCGAGCTCTACGTATTAATTAAGGCCGGCCAGGCCCGGGCTAGTCTCTTTTTCCAAT TTGCCACCGTGTAGCATTTTGTTGT-3′(SEQ ID NO: 3) DS249 5′-GTCAGGATCCTACGTACCCGGGGATATCATTATCATCTTTGTCGTGGTCATCTTGTGTG-3′ (SEQ ID NO: 4) DS2505′-GTCAGGATCCTACGTACCCGGGTAAGGCGTT CGTGCAGTGTGACGAATATAGCG-3′(SEQ ID NO: 5) DS251 5′-GTCAGAATTCGAGCTCTACGTATTAATTAAGGCCGGCCAGGCCCGGGCCCGTATGGACATACATA TATATATATATATATATATATATTTTGTTACGCG-3′ (SEQ ID NO: 6) DS252 5′-GTCAGAATTCGAGCTCTACGTATTAATTAAGGCCGGCCAGGCCCGGGCTTGTTGCAAGCAGCATG TCTAATTGGTAATTTTAAAGCTGCC-3′(SEQ ID NO: 7) DS267 5′-GTCAGAATTCGAGCTCTACGTATTAATTAAGGCCGGCCAGGCCCGGGCCCGTATGGACATACATA TATATATATATATATATATATATATATTTTGTTACGCG-3′ (SEQ ID NO: 8)

TABLE 5 Oligonucleotide Primers for DNASequencing S. cerevisiae PDI1 Genes Primer Sequence DS2535′-CCTCCCTGCTGCTCGCC-3′ (SEQ ID NO: 9) DS254 5′-CTGTAAGAACATGGCTCC-3′(SEQ ID NO: 10) DS255 5′-CTCGATCGATTACGAGGG-3′ (SEQ ID NO: 11) DS2565′-AAGAAAGCCGATATCGC-3′ (SEQ ID NO: 12) DS257 5′-CAACTCTCTGAAGAGGCG-3′(SEQ ID NO: 13) DS258 5′-CAACGCCACATCCGACG-3′ (SEQ ID NO: 14) DS2595′-GTAATTCTGATCACTTTGG-3′ (SEQ ID NO: 15) DS2605′-GCACTTATTATTACTACGTGG-3′ (SEQ ID NO: 16) DS2615′-GTTTTCCTTGATGAAGTCG-3′ (SEQ ID NO: 17) DS262 5′-GTGACCACACCATGGGGC-3′(SEQ ID NO: 18) DS263 5′-GTTGCCGGCGTGTCTGCC-3′ (SEQ ID NO: 19) DS2645′-TTGAAATCATCGTCTGCG-3′ (SEQ ID NO: 20) DS265 5′-CGGCAGTTCTAGGTCCC-3′(SEQ ID NO: 21) DS266 5′-CCACAGCCTCTTGTTGGG-3′ (SEQ ID NO: 22) M13/pUC 5′-GTTTTCCCAGTCACGAC-3′ Primer (-40) (SEQ ID NO: 23)

Plasmids pDB2941 (FIG. 28 of WO 2005/061718) and pDB2942 (FIG. 29 of WO2005/061718) were constructed similarly using the PCR primers describedin Tables 3 and 4, and by cloning the approximately 1.90-kb and 1.85-kbEcoRI-BamHI fragments, respectively, into YIplac211. The correct DNAsequences were confirmed for the PDI1 genes in pDB2941 and pDB2942.

The S. cerevisiae SKQ2n PDI1 gene sequence was PCR amplified fromplasmid DNA containing the PDI1 gene from pMA3a:C7 (U.S. Pat. No.6,291,205), also known as Clone C7 (Crouzet & Tuite, 1987, supra;Farquhar et al, 1991, supra). The SKQ2n PDI1 gene was amplified usingoligonucleotide primers DS248 and DS250 (Tables 3 and 4). Theapproximately 2.01-kb PCR product was digested with EcoRI and BamHI andligated into YIplac211 (Gietz & Sugino, 1988, Gene, 74, 527-534) thathas been cut with EcoRI and BamHI, to produce plasmid pDB2943 (FIG. 30of WO 2005/061718). The 5′ end of the SKQ2n PDI1 sequence is analogousto a blunt-ended SpeI-site extended to include the EcoRI, SacI, SnaBI,PacI, FseI, SfiI and SmaI sites, the 3′ end extends up to a siteanalogous to a blunt-ended Bsu36I site, extended to include a SmaI,SnaBI and BamHI sites. The PDI1 promoter length is approximately 210 bp.The entire DNA sequence was determined for the PDI1 fragment usingoligonucleotide primers given in Table 5. This confirmed the presence ofa coding sequence for the PDI protein of S. cerevisiae strain SKQ2n(NCBI accession number CAA38402), but with a serine residue at position114 (not an arginine residue as previously published). Similarly, in thesame way as in the S. cerevisiae S288c sequence in pDB2939, pDB2943 alsohad a missing ‘G’ from within the DS248 sequence, which is marked inbold in Table 4.

Plasmids pDB2963 (FIG. 31 of WO 2005/061718) and pDB2945 (FIG. 32 of WO2005/061718) were constructed similarly using the PCR primers describedin Tables 3 and 4, and by cloning the approximately 1.94-kb and 1.87-kbEcoRI-BamHI fragments, respectively, into YIplac211. The expected DNAsequences were confirmed for the PDI1 genes in pDB2963 and pDB2945, witha serine codon at the position of amino acid 114.

The Construction of pSAC35-Based rHA Expression Plasmids with DifferentPDI1 Genes Inserted at the XcmI-Site after REP2:

pSAC35-based plasmids were constructed for the co-expression of rHA withdifferent PDI1 genes (Table 6).

TABLE 6 pSAC35-based plasmids for co-expression of rHA with differentPDI1 genes Heterologous Protein Plasmid PDI1 Gene at XcmI-site afterREP2 Expression Cassette Plasmid Base Source Promoter TerminatorOrientation (at NotI-site) pDB2982 pSAC35 SKQ2n Long → Bsu36I A rHApDB2983 pSAC35 SKQ2n Long → Bsu36I B rHA pDB2984 pSAC35 SKQ2n Medium →Bsu36I A rHA pDB2985 pSAC35 SKQ2n Medium → Bsu36I B rHA pDB2986 pSAC35SKQ2n Short → Bsu36I A rHA pDB2987 pSAC35 SKQ2n Short → Bsu36I B rHApDB2976 pSAC35 S288c Long → Bsu36I A rHA pDB2977 pSAC35 S288c Long →Bsu36I B rHA pDB2978 pSAC35 S288c Medium → Bsu36I A rHA pDB2979 pSAC35S288c Medium → Bsu36I B rHA pDB2980 pSAC35 S288c Short → Bsu36I A rHApDB2981 pSAC35 S288c Short → Bsu36I B rHA

The rHA expression cassette from pDB2243 (FIG. 33 of WO 2005/061718, asalso described in WO 00/44772) was first isolated on a 2,992-bp NotIfragment, which subsequently was cloned into the NotI-site of pDB2688(FIG. 4 of WO 2005/061718) to produce pDB2693 (FIG. 34 of WO2005/061718). pDB2693 was digested with SnaBI, treated with calfintestinal alkaline phosphatase, and ligated with SnaBI fragmentscontaining the PDI1 genes from pDB2943, pDB2963, pDB2945, pDB2939,pDB2941 and pDB2942. This produced plasmids pDB2976 to pDB2987 (FIGS. 35to 46 of WO 2005/061718). PDI1 transcribed in the same orientation asREP2 was designated “orientation A”, in whereas PDI1 transcribed inopposite orientation to REP2 was designated “orientation B” (Table 6).

The Construction of pSAC35-Based Transferrin Expression Plasmids withDifferent PDH Genes Inserted at the XcmI-Site after REP2:

pSAC35-based plasmids were constructed for the co-expression ofrecombinant transferrin (N413Q, N611 Q) with different PDI1 genes (Table7).

TABLE 7 pSAC35-based plasmids for co-expression of transferrin withdifferent PDI1 genes Heterologous Protein Plasmid PDI1 Gene at XcmI-siteafter REP2 Expression Cassette Plasmid Base Source Promoter TerminatorOrientation (at NotI-site) pDB2929 pSAC35 SKQ2n Long → Bsu36I A rTf(N413Q, N611Q) pDB3085 pSAC35 S288c Long → Bsu36I A rTf (N413Q, N611Q)pDB3086 pSAC35 S288c Medium → Bsu36I A rTf (N413Q, N611Q) pDB3087 pSAC35S288c Short → Bsu36I A rTf (N413Q, N611Q)

In order to achieve this, the NotI expression cassettes for rHAexpression were first deleted from pDB2976, pDB2978, and pDB2980 by NotIdigestion and circularisation of the vector backbone. This producedplasmids pDB3081 (FIG. 47 of WO 2005/061718), pDB3083 (FIG. 48 of WO2005/061718) and pDB3084 (FIG. 49 of WO 2005/061718) as described inTable 8.

TABLE 8 pSAC35-based plasmids with different PDI1 genes HeterologousProtein Plasmid PDI1 Gene at XcmI-site after REP2 Expression CassettePlasmid Base Source Promoter Terminator Orientation (at NotI-site)pDB2690 pSAC35 SKQ2n Long → Bsu36I A None pDB3081 pSAC35 S288c Long →Bsu36I A None pDB3083 pSAC35 S288c Medium → Bsu36I A None pDB3084 pSAC35S288c Short → Bsu36I A None

The 3,256-bp NotI fragment from pDB2928 (FIG. 11 of WO 2005/061718) wascloned into the NotI-sites of pDB3081, pDB3083 and pDB3084, such thattranscription from the transferrin gene was in the same direction asLEU2. This produced plasmids pDB3085 (FIG. 50 of WO 2005/061718),pDB3086 (FIG. 51 of WO 2005/061718) and pDB3087 (FIG. 52 of WO2005/061718) as described in Table 7.

Example 7 Insertion and Optimisation of a PDH Gene in the 2 μm-LikePlasmid Increased the Secretion of Recombinant Human Serum Albumin byVarious Different S. cerevisiae Strains

The S. cerevisiae strains JRY188 cir⁰, MT302/28B cir⁰, 5150-2B cir⁰,CB11-63 cir⁰ (all described above), AH22 cir⁰ (Mead et al., 1986, Mol.Gen. Genet., 205, 417-421) and DS569 cir⁰ (Sleep et al., 1991,Bio/Technology, 9, 183-187) were transformed to leucine prototrophy witheither pDB2244 (WO 00/44772), pDB2976 (FIG. 35 of WO 2005/061718),pDB2978 (FIG. 37 of WO 2005/061718) or pDB2980 (FIG. 39 of WO2005/061718) using a modified lithium acetate method (Sigma yeasttransformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J.Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)).Transformants were selected on BMMD-agar plates with appropriatesupplements, and were subsequently patched out on BMMD-agar plates withappropriate supplements.

Transformants of each strain were inoculated into 10 mL YEPD in 50 mLshake flasks and incubated in an orbital shaker at 30° C., 200 rpm for4-days. Culture supernatants were harvested and the recombinant albumintitres compared by rocket immunoelectrophoresis (FIGS. 11 and 12). Theresults indicated that the albumin titres in the culture supernatantsfrom all the yeast strains were higher when PDI1 was present in the 2 μmplasmid than when it was not (pDB2244). The albumin titre in the culturesupernatants in the absence of PDI1 on the plasmid was dependant uponwhich yeast strain was selected as the expression host, however, in mostexamples tested the largest increase in expression was observed whenPDI1 with the long promoter (˜210-bp) was present in the 2 μm plasmid(pDB2976). Modifying the PDI1 promoter by shortening, for example todelete regulation sites, had the affect of controlling the improvement.For one yeast strain, known to be a high rHA producing strain (DS569) ashorter promoter was preferred for optimal expression.

Example 8 PDI1 on the 2 μm-Based Plasmid Enhanced the Secretion ofRecombinant Albumin Fusions

The affect of co-expression of the S. cerevisiae SKQ2n PDI1 gene withthe long promoter (˜210-bp) upon the expression of recombinant albuminfusions was investigated.

The plasmids defined in Table 9 below were generated as described inExample 9 of WO 2005/061718, the contents of which are incorporatedherein by reference.

TABLE 9 Summary of plasmids encoding albumin fusion proteins Plasmidname Albumin fusion With PDI1 Without PDI1 endostatin-albumin pDB3100PDB3099 angiostatin-albumin pDB3107 pDB2765 Kringle5-(GGS)₄GG-albuminpDB3104 pDB2773 DX-890-(GGS)₄GG-albumin pDB3102 pDB3101DPI-14-(GGS)₄GG-albumin pDB3103 pDB2679 Axokine ™-(GGS)₄GG-albuminpDB3106 pDB2618 human IL10-(GGS)4-GG-albumin pDB3105 pDB2621

The same control yeast strain as used in previous examples wastransformed to leucine prototrophy using a modified lithium acetatemethod (Sigma yeast transformation kit, YEAST-1, protocol 2; (Ito et al,1983, J. Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)).Transformants were selected on BMMD-agar plates, and were subsequentlypatched out on BMMD-agar plates. Cryopreserved trehalose stocks wereprepared from 10 mL BMMD shake flask cultures (24 hrs, 30° C., 200 rpm).

Transformants of each strain were inoculated into 10 mL BMMD in 50 mLshake flasks and incubated in an orbital shaker at 30° C., 200 rpm for4-days. Culture supernatants were harvested and the recombinant albuminfusion titres compared by rocket immunoelectrophoresis (FIG. 13). Theresults indicated that the albumin fusion titre in the culturesupernatants from yeast strain was higher when PDI1 was present in the 2μm plasmid than when it was not.

The increase in expression of the albumin fusions detected by rocketimmunoelectrophoresis was further studied by SDS-PAGE analysis. BMMDshake flask cultures of YBX7 expressing various albumin-fusions weregrown for 4-days in an orbital shaker at 30° C., 200 rpm. A sample ofthe culture supernatant was analysed by SDS-PAGE (FIG. 14). A proteinband of the expected size for the albumin fusion under study wasobserved increase in abundance.

Example 9 Co-Expression of S. cerevisiae ORM2 and RecombinantTransferrin on a 2 μm-Based Plasmid

The S. cerevisiae Control Strain and Strain A (as described in Example3) were selected to investigate the effect on transferrin secretion whenthe transferrin and ORM2 genes were co-expressed from the 2 μm-basedplasmids. The Control Strain and Strain A were transformed to leucineprototrophy by plasmids pDB3090, pDB3092 and pBD3093 (containingexpression cassettes for rTf (N413Q, N611Q) and for ORM2), as well as acontrol plasmid pDB2931 (containing the rTf (N413Q, N611Q) expressioncassette without ORM2). The construction of these plasmids is describedin Example 10 of WO 2005/061718, the contents of which are incorporatedherein by reference. Transformants were selected on BMMD agar andpatched out on BMMD agar for subsequent analysis.

To investigate the effect of ORM2 co-expression on transferrinsecretion, 10 mL selective (BMMD) and non-selective (YEPD) liquid mediawere inoculated with strains containing the ORM2/transferrinco-expression plasmids. The shake flask culture was then incubated at30° C. with shaking (200 rpm) for 4 days. The relative level oftransferrin secretion was determined by rocket gel immunoelectrophoresis(RIE) (FIG. 15).

Levels of transferrin secreted from Control Strain [pDB3090] and ControlStrain [pDB3092] were greater than the levels from Control Strain[pDB2931] in both BMMD and YEPS media. Similarly, the levels oftransferrin secreted from both Strain A [pDB3090] and Strain A [pDB3093]were greater than the levels from Strain A [pDB2931] in both BMMD andYEPS media. Transferrin secretion from all Strain A transformants washigher than the Control Strain transformants grown in the same media.Strain A contains an additional copy of PDI1 in the genome, whichenhanced transferrin secretion. Therefore in Strain A, the increasedexpression of ORM2 and PDI1 had a cumulative effect on the secretion oftransferrin.

Example 10 Co-Expression of S. cerevisiae PSE1 and RecombinantTransferrin on a 2 μm-Based Plasmid

The S. cerevisiae Control Strain was transformed to leucine prototrophyby plasmids, pDB3097 and pBD3098 (containing expression cassettes forrTf (N413Q, N611Q) and for PSE1), as well as a control plasmid pDB2931(containing the rTf (N413Q, N611Q) expression cassette without PSE1).The construction of these plasmids are described in Example 11 of WO2005/061718, the contents of which are incorporated herein by reference.Transformants were selected on BMMD agar and patched out on BMMD agarfor subsequent analysis.

To investigate the effect of PSE1 expression on transferrin secretion,flasks containing 10 mL selective (BMMD) liquid media were inoculatedwith strains containing the PSE1/transferrin co-expression plasmids. Theshake flask culture was then incubated at 30° C. with shaking (200 rpm)for 4 days. The relative level of transferrin secretion was determinedby rocket gel immunoelectrophoresis (RIE) (FIG. 16).

Levels of transferrin secreted from Control Strain [pDB3097] and ControlStrain [pDB3098] were greater than the levels from Control Strain[pDB2931] in BMMD media. Therefore, expression of PSE1 from the 2μm-based plasmids had enhanced transferrin secretion from S. cerevisiae.Transferrin secretion was improved with the PSE1 gene transcribed ineither direction relative to the REP2 gene in pDB3097 and pDB3098.

Example 11 Co-Expression of S. cerevisiae SSA1 and RecombinantTransferrin on a 2 μm-Based Plasmid

The S. cerevisiae Control Strain was transformed to leucine prototrophyby plasmids, pDB3094 and pBD3095 (containing expression cassettes forrTf (N413Q, N611Q) and for SSA1), as well as a control plasmid pDB2931(containing the rTf (N413Q, N611Q) expression cassette without SSA1).The construction of these plasmids are described in Example 12 of WO2005/061718, the contents of which are incorporated herein by reference.Transformants were selected on BMMD agar and patched out on BMMD agarfor subsequent analysis.

To investigate the effect of SSA1 expression on transferrin secretion,flasks containing 10 mL selective (BMMD) liquid media were inoculatedwith strains containing the SSA1/transferrin co-expression plasmids. Theshake flask cultures were incubated at 30° C. with shaking (200 rpm) for4 days. The relative level of transferrin secretion was determined byrocket gel immunoelectrophoresis (RIE) (FIG. 17).

Levels of transferrin secreted from Control Strain [pDB3095] weregreater than the levels from Control Strain [pDB2931] and Control Strain[pDB3094] in BMMD media. Therefore, expression of SSA1 from the 2μm-based plasmids had enhanced transferrin secretion from S. cerevisiae.Transferrin secretion was improved with the SSA1 gene transcribed in theopposite direction relative to the REP2 gene in pDB3094.

Example 12 PDH Gene Disruption, Combined with a PDH Gene on the 2μm-Based Plasmid Enhanced the Secretion of Recombinant Albumin andPlasmid Stability

Single stranded oligonucleotide DNA primers listed in Table 11 weredesigned to amplify a region upstream of the yeast PDI1 coding regionand another a region downstream of the yeast PDI1 coding region.

TABLE 11 Oligonucleotide primers Primer Description Sequence DS299 5′PDI1 5′-CGTAGCGGCCGCCTGAAAG primer, GGGTTGACCGTCCGTCGGC-3′ 38mer(SEQ ID NO: 24) DS300 5′ PDI1 5′-CGTAAAGCTTCGCCGCCCG primer,ACAGGGTAACATATTATCAC-3′ 40mer (SEQ ID NO: 25) DS301 3′ PDI15′-CGTAAAGCTTGACCACGTA primer, GTAATAATAAGTGCATGGC-3′ 38mer(SEQ ID NO: 26) DS302 3′ PDI1 5′-CGTACTGCAGATTGGATAG primer,TGATTAGAGTGTATAGTCCCG 41mer G-3′ (SEQ ID NO: 27) DS303 18mer5′-GGAGCGACAAACCTTTC G-3′ (SEQ ID NO: 28) DS304 20mer5′-ACCGTAATAAAAGATGGCT G-3′ (SEQ ID NO: 29) DS305 24mer5′-CATCTTGTGTGTGAGTATG GTCGG-3′ (SEQ ID NO: 30) DS306 14mer5′-CCCAGGATAATTTTCAG G-3′ (SEQ ID NO: 31)

Primers DS299 and DS300 amplified the 5′ region of PDI1 by PCR, whileprimers DS301 and DS302 amplified a region 3′ of PDI1, using genomic DNAderived S288c as a template. The PCR conditions were as follows: 1 μLS288c template DNA (at 0.01 ng/μL, 0.1 ng/μL, 1 ng/μL, 10 ng/μL and 100ng/μL), 5 μL 10×Buffer (Fast Start Taq+Mg, (Roche)), 1 μL 10 mM dNTP's,5 μL each primer (2 μM), 0.4 μL Fast Start Taq, made up to 504 with H₂O.PCRs were performed using a Perkin-Elmer Thermal Cycler 9700. Theconditions were: denature at 95° C. for 4 min [HOLD], then [CYCLE]denature at 95° C. for 30 seconds, anneal at 45° C. for 30 seconds,extend at 72° C. for 45 seconds for 20 cycles, then [HOLD] 72° C. for 10min and then [HOLD] 4° C. The 0.22 kbp PDI1 5′ PCR product was cut withNotI and HindIII, while the 0.34 kbp PDI1 3′ PCR product was cut withHindIII and PstI.

Plasmid pMCS5 (Hoheisel, 1994, Biotechniques 17, 456-460) (FIG. 85 of WO2005/061718) was digested to completion with HindIII, blunt ended withT4 DNA polymerase plus dNTPs and religated to create pDB2964 (FIG. 86 ofWO 2005/061718).

Plasmid pDB2964 was HindIII digested, treated with calf intestinalphosphatase, and ligated with the 0.22 kbp PDI1 5′ PCR product digestedwith NotI and HindIII and the 0.34 kbp PDI1 3′ PCR product digested withHindIII and PstI to create pDB3069 (FIG. 87 of WO 2005/061718) which wassequenced with forward and reverse universal primers and the DNAsequencing primers DS303, DS304, DS305 and DS306 (Table 11).

Primers DS234 and DS235 (Table 12) were used to amplify the modifiedTRP1 marker gene from YIplac204 (Gietz & Sugino, 1988, Gene, 74,527-534), incorporating HindIII restriction sites at either end of thePCR product. The PCR conditions were as follows: 14 template YIplac204(at 0.01 ng/μL, 0.1 ng/μL, 1 ng/μL, 10 ng/μL and 100 ng/μL, 5 μL10×Buffer (Fast Start Taq+Mg, (Roche)), 1 μL 10 mM dNTP's, 5 μL eachprimer (2 μM), 0.44 Fast Start Taq, made up to 50 μL with H₂O. PCRs wereperformed using a Perkin-Elmer Thermal Cycler 9600. The conditions were:denature at 95° C. for 4 min [HOLD], then [CYCLE] denature at 95° C. for30 seconds, anneal for 45 seconds at 45° C., extend at 72° C. for 90 secfor 20 cycles, then [HOLD] 72° C. for 10 min and then [HOLD] 4° C. The0.86 kbp PCR product was digested with HindIII and cloned into theHindIII site of pMCS5 to create pDB2778 (FIG. 88 of WO 2005/061718).Restriction enzyme digestions and sequencing with universal forward andreverse primers as well as DS236, DS237, DS238 and DS239 (Table 12)confirmed that the sequence of the modified TRP1 gene was correct.

TABLE 12 Oligonucleotide primers Primer Description Sequence DS230TRP1 5′ 5′-TAGCGAATTCAATCAGTA UTR AAAATCAACGG-3′ (SEQ ID NO: 32) DS231TRP1 5′ 5′-GTCAAAGCTTCAAAAAAA UTR GAAAAGCTCCGG-3′ (SEQ ID NO: 33) DS232TRP1 3′ 5′-TAGCGGATCCGAATTCGG UTR CGGTTGTTTGCAAGACCGAG-3′(SEQ ID NO: 34) DS233 TRP1 3′ 5′-GTCAAAGCTTTAAAGATA UTRATGCTAAATCATTTGG-3′ (SEQ ID NO: 35) DS234 TRP1 5′-TGACAAGCTTTCGGTCGAAAAAAGAAAAGGAGAGG-3′ (SEQ ID NO: 36) DS235 TRP1 5′-TGACAAGCTTGATCTTTTATGCTTGCTTTTC-3′ (SEQ ID NO: 37) DS236 TRP1 5′-AATAGTTCAGGCACTCCG-3′(SEQ ID NO: 38) DS237 TRP1 5′-TGGAAGGCAAGAGAGCC-3′ (SEQ ID NO: 39) DS238TRP1 5′-TAAAATGTAAGCTCTCGG-3′ (SEQ ID NO: 40) DS239 TRP15′-CCAACCAAGTATTTCGG-3′ (SEQ ID NO: 41) CED005 ΔTRP15′-GAGCTGACAGGGAAATGG TC-3′ (SEQ ID NO: 42) CED006 ΔTRP15′-TACGAGGATACGGAGAGA GG-3′ (SEQ ID NO: 43)

The 0.86 kbp TRP1 gene was isolated from pDB2778 by digestion withHindIII and cloned into the HindIII site of pDB3069 to create pDB3078(FIG. 89 of WO 2005/061718) and pDB3079 (FIG. 90 of WO 2005/061718). A1.41 kb pdi1::TRP1 disrupting DNA fragment was isolated from pDB3078 orpDB3079 by digestion with NotI/PstI.

Yeast strains incorporating a TRP1 deletion (trp1Δ) were to beconstructed in such a way that no homology to the TRP1 marker gene(pDB2778) should left in the genome once the trp1Δ had been created, sopreventing homologous recombination between future TRP1 containingconstructs and the TRP1 locus. In order to achieve the total removal ofthe native TRP1 sequence from the genome of the chosen host strains,oligonucleotides were designed to amplify areas of the 5′ UTR and 3′ UTRof the TRP1 gene outside of TRP1 marker gene present on integratingvector YIplac204 (Gietz & Sugino, 1988, Gene, 74, 527-534). TheYIplac204 TRP1 marker gene differs from the native/chromosomal TRP1 genein that internal HindIII, PstI and XbaI sites were removed by sitedirected mutagenesis (Gietz & Sugino, 1988, Gene, 74, 527-534). TheYIplac204 modified TRP1 marker gene was constructed from a 1.453 kbpblunt-ended genomic fragment EcoRI fragment, which contained the TRP1gene and only 102 bp of the TRP1 promoter (Gietz & Sugino, 1988, Gene,74, 527-534). Although this was a relatively short promoter sequence itwas clearly sufficient to complement trp1 auxotrophic mutations (Gietz &Sugino, 1988, Gene, 74, 527-534). Only DNA sequences upstream of theEcoRI site, positioned 102 bp 5′ to the start of the TRP1 ORF were usedto create the 5′ TRP1 UTR. The selection of the 3′ UTR was less criticalas long as it was outside the 3′ end of the functional modified TRP1marker, which was chosen to be 85 bp downstream of the translation stopcodon.

Single stranded oligonucleotide DNA primers were designed andconstructed to amplify the 5′ UTR and 3′ UTR regions of the TRP1 gene sothat during the PCR amplification restriction enzyme sites would beadded to the ends of the PCR products to be used in later cloning steps.Primers DS230 and DS231 (Table 12) amplified the 5′ region of TRP1 byPCR, while primers DS232 and DS233 (Table 12) amplified a region 3′ ofTRP1, using S288c genomic DNA as a template. The PCR conditions were asfollows: 14 template S288c genomic DNA (at 0.01 ng/μL, 0.1 ng/μL, 1ng/μL, 10 ng/μL and 100 ng/μL), 5 μL 10×Buffer (Fast Start Taq+Mg,(Roche)), 1 μL 10 mM dNTP's, 54 each primer (2 μM), 0.44 Fast Start Taq,made up to 50 μL with H₂O. PCRs were performed using a Perkin-ElmerThermal Cycler 9600. The conditions were: denature at 95° C. for 4 min[HOLD], then [CYCLE] denature at 95° C. for 30 seconds, anneal for 45seconds at 45° C., extend at 72° C. for 90 sec for 20 cycles, then[HOLD] 72° C. for 10 min and then [HOLD] 4° C.

The 0.19 kbp TRP1 5′ UTR PCR product was cut with EcoRI and HindIII,while the 0.2 kbp TRP1 3′ UTR PCR product was cut with BamHI and HindIIIand ligated into pAYE505 linearised with BamHI/EcoRI to create plasmidpDB2777 (FIG. 91 of WO 2005/061718). The construction of pAYE505 isdescribed in WO 95/33833. DNA sequencing using forward and reverseprimers, designed to prime from the plasmid backbone and sequence thecloned inserts, confirmed that in both cases the cloned 5′ and 3′ UTRsequences of the TRP1 gene had the expected DNA sequence. PlasmidpDB2777 contained a TRP1 disrupting fragment that comprised a fusion ofsequences derived from the 5′ and 3′ UTRs of TRP1. This 0.383 kbp TRP1disrupting fragment was excised from pDB2777 by complete digestion withEcoRI.

Yeast strain DXY1 (Kerry-Williams et al., 1998, Yeast, 14, 161-169) wastransformed to leucine prototrophy with the albumin expression plasmidpDB2244 using a modified lithium acetate method (Sigma yeasttransformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J.Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)) to createyeast strain DXY1 [pDB2244]. The construction of the albumin expressionplasmid pDB2244 is described in WO 00/44772. Transformants were selectedon BMMD-agar plates, and were subsequently patched out on BMMD-agarplates. Cryopreserved trehalose stocks were prepared from 10 mL BMMDshake flask cultures (24 hrs, 30° C., 200 rpm).

DXY1 [pDB2244] was transformed to tryptophan autotrophy with the 0.383kbp EcoRI TRP1 disrupting DNA fragment from pDB2777 using a nutrientagar incorporating the counter selective tryptophan analogue,5-fluoroanthranilic acid (5-FAA), as described by Toyn et al., (2000Yeast 16, 553-560). Colonies resistant to the toxic effects of 5-FAAwere picked and streaked onto a second round of 5-FAA plates to confirmthat they really were resistant to 5-FAA and to select away from anybackground growth. Those colonies which grew were then were re-patchedonto BMMD and BMMD plus tryptophan to identify which were tryptophanauxotrophs.

Subsequently colonies that had been shown to be tryptophan auxotrophswere selected for further analysis by transformation with YCplac22(Gietz & Sugino, 1988, Gene, 74, 527-534) to ascertain which isolateswere trp1.

PCR amplification across the TRP1 locus was used to confirm that thetrp⁻ phenotype was due to a deletion in this region. Genomic DNA wasprepared from isolates identified as resistant to 5-FAA and unable togrow on minimal media without the addition of tryptophan. PCRamplification of the genomic TRP1 locus with primers CED005 and CED006(Table 12) was achieved as follows: 14 template genomic DNA, 5 μL10×Buffer (Fast Start Taq+Mg, (Roche)), 1 μL 10 mM dNTP's, 54 eachprimer (2 μM), 0.44 Fast Start Taq, made up to 50 μL with H₂O. PCRs wereperformed using a Perkin-Elmer Thermal Cycler 9600. The conditions were:denature at 94° C. for 10 min [HOLD], then [CYCLE] denature at 94° C.for 30 seconds, anneal for 30 seconds at 55° C., extend at 72° C. for120 sec for 40 cycles, then [HOLD] 72° C. for 10 min and then [HOLD] 4°C. PCR amplification of the wild type TRP1 locus resulted in a PCRproduct of 1.34 kbp in size, whereas amplification across the deletedTRP1 region resulted in a PCR product 0.84 kbp smaller at 0.50 kbp. PCRanalysis identified a DXY1 derived trp⁻ strain (DXY1 trp1Δ [pDB2244]) ashaving the expected deletion event.

The yeast strain DXY1 trp1Δ [pDB2244] was cured of the expressionplasmid pDB2244 as described by Sleep et al., (1991, Bio/Technology, 9,183-187). DXY1 trp1Δ cir⁰ was re-transformed the leucine prototrophywith either pDB2244, pDB2976, pDB2977, pDB2978, pDB2979, pDB2980 orpDB2981 using a modified lithium acetate method (Sigma yeasttransformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J.Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)).Transformants were selected on BMMD-agar plates supplemented withtryptophan, and were subsequently patched out on BMMD-agar platessupplemented with tryptophan. Cryopreserved trehalose stocks wereprepared from 10 mL BMMD shake flask cultures supplemented withtryptophan (24 hrs, 30° C., 200 rpm).

The yeast strains DXY1 trp1Δ [pDB2976], DXY1 trp1Δ [pDB2977], DXY1 trp1Δ[pDB2978], DXY1 trp1Δ [pDB2979], DXY1 trp1Δ [pDB2980] or DXY1 trp1Δ[pDB2981] was transformed to tryptophan prototrophy using the modifiedlithium acetate method (Sigma yeast transformation kit, YEAST-1,protocol 2; (Ito et al, 1983, J. Bacteriol., 153, 163; Elble, 1992,Biotechniques, 13, 18)) with a 1.41 kb pdi1::TRP1 disrupting DNAfragment was isolated from pDB3078 by digestion with NotI/PstI.Transformants were selected on BMMD-agar plates and were subsequentlypatched out on BMMD-agar plates.

Six transformants of each strain were inoculated into 10 mL YEPD in 50mL shake flasks and incubated in an orbital shaker at 30° C., 200 rpmfor 4-days. Culture supernatants and cell biomass were harvested.Genomic DNA was prepared (Lee, 1992, Biotechniques, 12, 677) from thetryptophan prototrophs and DXY1 [pDB2244]. The genomic PDI1 locusamplified by PCR of with primers DS236 and DS303 (Table 11 and 12) wasachieved as follows: 1 μL template genomic DNA, 5 μL 10×Buffer (FastStart Taq+Mg, (Roche)), 1 μL 10 mM dNTP's, 5 μL each primer (2 μM), 0.4μL Fast Start Taq, made up to 50 μL with H₂O. PCRs were performed usinga Perkin-Elmer Thermal Cycler 9700. The conditions were: denature at 94°C. for 4 min [HOLD], then [CYCLE] denature at 94° C. for 30 seconds,anneal for 30 seconds at 50° C., extend at 72° C. for 60 sec for 30cycles, then [HOLD] 72° C. for 10 min and then [HOLD] 4° C. PCRamplification of the wild type PDI1 locus resulted in no PCR product,whereas amplification across the deleted PDI1 region resulted in a PCRproduct 0.65 kbp. PCR analysis identified that all 36 potentialpdi1::TRP1 strains tested had the expected pdi1::TRP1 deletion.

The recombinant albumin titres were compared by rocketimmunoelectrophoresis (FIG. 18). Within each group, all six pdi1::TRP1disruptants of DXY1 trp1Δ [pDB2976], DXY1 trp1Δ [pDB2978], DXY1 trp1Δ[pDB2980], DXY1 trp1Δ [pDB2977] and DXY1 trp1Δ [pDB2979] had verysimilar rHA productivities. Only the six pdi1::TRP1 disruptants of DXY1trp1Δ [pDB2981] showed variation in rHA expression titre. The sixpdi1::TRP1 disruptants indicated in FIG. 18 were spread onto YEPD agarto isolate single colonies and then re-patched onto BMMD agar.

Three single celled isolates of DXY1 trp1Δ pdi1::TRP1 [pDB2976], DXY1trp1Δ pdi1::TRP1 [pDB2978], DXY1 trp1Δ pdi1::TRP1 [pDB2980], DXY1 trp1Δpdi1::TRP1 [pDB2977], DXY1 trp1Δ pdi1::TRP1 [pDB2979] and DXY1 trp1Δpdi1::TRP1 [pDB2981] along with DXY1 [pDB2244], DXY1 [pDB2976], DXY1[pDB2978], DXY1 [pDB2980], DXY1 [pDB2977], DXY1 [pDB2979] and DXY1[pDB2981] were inoculated into 10 mL YEPD in 50 mL shake flasks andincubated in an orbital shaker at 30° C., 200 rpm for 4-days. Culturesupernatants were harvested and the recombinant albumin titres werecompared by rocket immunoelectrophoresis (FIG. 19). The thirteen wildtype PDI1 and pdi1::TRP1 disruptants indicated in FIG. 19 were spreadonto YEPD agar to isolate single colonies. One hundred single celledcolonies from each strain were then re-patched onto BMMD agar or YEPDagar containing a goat anti-HSA antibody to detect expression ofrecombinant albumin (Sleep et al., 1991, Bio/Technology, 9, 183-187) andthe Leu+/rHA+, Leu+/rHA−, Leu−/rHA+ or Leu−/rHA− phenotype of eachcolony scored (Table 13).

TABLE 13 PDI1 pdi1::TRP1 Leu+ Leu− Leu+ Leu− Leu+ Leu− Leu+ Leu− rHA+rHA+ rHA− rHA− rHA+ rHA+ rHA− rHA− pDB2244 100 0 0 0 pDB2976 7 0 47 4697 0 3 0 pDB2978 86 0 0 14 100 0 0 0 pDB2980 98 0 0 2 100 0 0 0 pDB29770 0 4 96 100 0 0 0 pDB2979 69 0 6 25 100 0 0 0 pDB2981 85 0 0 15 92 0 08

These data indicate plasmid retention is increased when the PDI1 gene isused as a selectable marker on a plasmid in a host strain having nochromosomally encoded PDI, even in a non-selective medium such as theexemplified rich medium.

Example 13 Construction of the pSAC35-Based Expression VectorspDB3175-pDB3182 for Co-Expression of PDI1 with Recombinant Human Albuminor Transferrin (N413Q, N611Q) from the SnaBI/NotI-Site in the 2 μmUL-Region

The NotI expression cassette from the pSAC35-based expression vector,pAYE316 (Sleep et al, 1991, Biotechnology (N.Y.), 9, 183-187), designedfor the secretion of recombinant human albumin, was cloned into theunique NotI-site of the E. coli cloning vector pBST(+) (Sleep et al,2001, Yeast, 18, 403-421) to produce plasmid pQC262e. pQC262e wassubsequently modified by site-directed mutagenesis (Kunkel et al, 1987,Methods Enzymol., 154, 367-382) with oligonucleotide LRE49 (Table 14) tointroduce a unique Asp718I-site immediately upstream of the NotI-site atthe ADH1 terminator region of the expression cassette.

TABLE 14 Mutagenic Oligonucleotide Primer Description Sequence LRE49Mutagenic 45mer 5′-GCTAGCGTCGACAAGCTTGCGG ADH1 terminatorCGCGGTACCGTGTGGAAGAACG-3′ region (SEQ ID NO: 44)

This produced plasmid pAYE560 (FIG. 21). The S. cerevisiae SKQ2n PDI1gene with the long (˜210-bp) promoter was isolated on 1.96-kb SmaIfragment from pDB2952 (FIG. 46 in WO 2005/061719, the contents of whichare incorporated herein by reference). The pDB2952 PDI1 fragment wascloned into the unique Asp718I-site of pAYE560, following digestion withAsp718I, filling the 3′-recessed ends using T4 DNA polymerase, and calfintestinal alkaline phosphatase treatment of the blunt-ended product.This produced plasmids pDB3171 (FIG. 22) with the PDI1 gene transcribedin the same direction as rHA, and pDB3172 (FIG. 23) with convergingtranscription of the PDI1 and rHA genes.

pDB3175 and pDB3176 (FIGS. 24 and 25) were produced by cloning the˜5.1-kb rHA→PDI1→NotI expression cassette from pDB3171 into pSAC35,which had been digested with NotI and calf intestinal alkalinephosphatase. pDB3177 and pDB3178 (FIGS. 26 and 27) were producedsimilarly by cloning the ˜5.1-kb NotI rHA→←PDI1 expression cassette frompDB3172 into pSAC35 digested with NotI and calf intestinal alkalinephosphatase.

To construct NotI expression cassettes for co-expression of recombinantunglycosylated human transferrin (N413Q, N611Q) and the S. cerevisiaeSKQ2n PDI1 gene with the long (˜210-bp) promoter, the ˜6.1-kb AfiII-SphIfragment from pDB3171 was ligated with the ˜2.4-kb AflII-SphI fragmentfrom pDB2928 (FIG. 11 of WO 2005/061718, the contents of which areincorporated herein by reference), thus replacing the rHA coding andadjacent sequences with those for transferrin (N413Q, N611Q) secretion.This produced plasmids pDB3173 (FIG. 28) with the PDI1 gene transcribedin the same direction as rTf (N413Q, N611Q), and pDB3174 (FIG. 29) withconverging transcription of the PDI1 and rTf (N413Q, N611Q) genes.

pDB3179 and pDB3180 (FIGS. 30 and 31) were produced by cloning the˜5.2-kb rTf→PDI1→NotI expression cassette from pDB3173 into pSAC35,which had been digested with NotI and calf intestinal alkalinephosphatase. pDB3181 and pDB3182 (FIGS. 32 and 33) were produced bycloning the ˜5.2-kb NotI rTf→←PDI1 expression cassette from pDB3174 intopSAC35 digested with NotI and calf intestinal alkaline phosphatase.

Example 14 S. cerevisiae PDI1 at the SnaBI/NotI-Site in the UL-Region ofpSAC35-Based Expression Vectors as a Selectable Marker in S. cerevisiaeStrain DXY1 Δtrp1 Pdi1::TRP1

The yeast strains DXY1 (Kerry-Williams et al., 1998, Yeast, 14, 161-169)and DXY1 Δtrp1 (see Example 13 of WO 2005/061718, the contents of whichare incorporated herein by reference) were transformed to leucineprototrophy with pSAC35-based plasmids pAYE316, pDB3175, pDB3176,pDB3177, pDB3178, pDB2931, pDB3179, pDB3180, pDB3181 and pDB3182 using amodified lithium acetate method (Sigma yeast transformation kit,YEAST-1, protocol 2; (Ito et al, 1983, J. Bacteriol., 153, 163; Elble,1992, Biotechniques, 13, 18)). Transformants were selected on BMMD-agarplates with appropriate supplements, and were subsequently patched outon BMMD-agar plates with appropriate supplements.

DXY1 Δtrp1 [pDB3175], DXY1 Δtrp1 [pDB3176], DXY1 Δtrp1 [pDB3177], DXY1Δtrp1 [pDB3178], DXY1 Δtrp1 [pDB3179], DXY1 Δtrp1 [pDB3180], DXY1 Δtrp1[pDB3181], and DXY1 Δtrp1 [pDB3182] were transformed to tryptophanprototrophy using the modified lithium acetate method (Sigma yeasttransformation kit, YEAST-1, protocol 2; (Ito et al, 1983, J.Bacteriol., 153, 163; Elble, 1992, Biotechniques, 13, 18)) with a1.41-kb pdi1::TRP1 disrupting DNA fragment isolated from pDB3078 bydigestion with NotI/PstI. (see Example 13 of WO 2005/061718).Transformants were selected on BMMD-agar plates and were subsequentlypatched out on BMMD-agar plates.

Disruption of the PDI1 gene with the TRP1 marker was confirmed bydiagnostic PCR amplification of an approximately 810-bp product usingoligonucleotide primers CF247 and DS236 (Table 15). CF247 binds in thePDI1 promoter region upstream of the disruption site and DS236 bindswithin the TRP1 gene.

TABLE 15 Oligonucleotide Sequencing Primers Primer Description SequenceCF247 PDI1 promoter 5′-GCGCGTTTTCATTAGTGCCC-3′ region, 20mer(SEQ ID NO: 45) DS236 TRP1 coding 5′-AAATAGTTCAGGCACTCCG-3′region, 19mer (SEQ ID NO: 38)

DXY1 Δtrp1, DXY1 Δtrp1 containing pDB3175-pDB3182 and putativepdi1::TRP1-disruptants were inoculated into 10 mL YEPD in 50 mL shakeflasks, and incubated in an orbital shaker at 30° C., 200 rpm for4-days. Genomic DNA was prepared (Lee, 1992, Biotechniques, 12, 677)from the biomass for subsequent use as template DNA in diagnostic PCR.

0.5 μL template genomic DNA, 2.5 μL 10×Buffer (Fast Start Taq+Mg,(Roche)), 0.5 μL 10 mM dNTP's, 2.5 μL each primer (2 μM), 0.2 μL FastStart Taq were mixed and made up to 254 with H₂O. PCRs were performedusing a Dyad™ DNA Engine Peltier thermal cycler (GRI) as follows;denaturation at 95° C. for 4 mins, then 25 cycles of 95° C. for 30 s,55° C. for 30 s and 72° C. for 1 min, followed by extension at 72° C.for 10 mins. A PCR product of ˜810-bp was only amplified from DNAcontaining the TRP1 gene integrated at the pdi1 locus. DXY1 Δtrp1pdi1::TRP1 containing pDB3175-pDB3182 were successfully identified. Asexpected, no PCR product was generated for the controls DXY1 Δtrp1 orDXY1 Δtrp1 containing pDB3175-pDB3182. DXY1 containing pDB3175-pDB3182were compared with DXY1 Δtrp1 pdi1::TRP1 containing pDB3175-pDB3182 forplasmid stability and secretion of recombinant human albumin ortransferrin (N413Q, N611Q) in YEPD shake flask culture. 10 mL YEPD shakeflasks were inoculated with the above strains and grown for 4-days at30° C., 200 rpm. Samples were spread onto YEPD-agar plates and grown tosingle colonies. Fifty randomly selected colonies were patched out inreplica onto BMMD and YEPD plates and incubated at 30° C. Plasmidstability was scored as the percentage of colonies able to grow on bothmedia. The results shown in Tables 16 and 17 demonstrated that all ofthe plasmids pDB3175-pDB3182 were less than 100% stable in DXY1,regardless of the relative orientations of the PDI1 and rTf/rHA genescloned at the SnaBI/NotI-site. However, 100% plasmid stability wasdetermined in all cases in DXY1 Δtrp1 pdi1::TRP1 containingpDB3175-pDB3182. Hence, use of PDI1 as the sole selectable marker at theSnaBI/NotI-site of pSAC35-based vectors resulted in 100% plasmidstability in rich media.

TABLE 16 Plasmid stability of pSAC35-based vectors containing arecombinant albumin gene and the S. cerevisiae PDI1 gene at theSnaBI/NotI-site in the UL- region in strains DXY1 and DXY1 Δtrp1pdi1::TRP1. 10 mL YEPD shake flasks were inoculated with DXY1 [pDB3175],DXY1 [pDB3176], DXY1 [pDB3177], DXY1 [pDB3178], DXY1 Δtrp1 pdi1::TRP1[pDB3175], DXY1 Δtrp1 pdi1::TRP1 [pDB3176], DXY1 Δtrp1 pdi1::TRP1[pDB3177], and DXY1 Δtrp1 pdi1::TRP1 [pDB3178] were grown for 4-days at30° C., 200 rpm. Samples were spread onto YEPD-agar plates and grown tosingle colonies. Fifty randomly selected colonies were patched out inreplica onto BMMD and YEPD plates and incubated at 30° C. Plasmidstability was scored as the percentage of colonies able to grow on bothmedia. Plasmid Stability (% Prototrophs) SnaBI/NotI DXY1 Δtrp1 PlasmidCassette* DXY1 DXY1 Δtrp1 pdi1::TRP1 pDB3175 LEU2 rHA PDI1 96 0 100 → →→ pDB3176 LEU2 PDI1 rHA 68 0 100 → ← ← pDB3177 LEU2 rHA PDI1 86 0 100 →→ ← pDB3178 LEU2 PDI1 rHA 28 0 100 → → ← *Arrows indicate the directionof transcription relative to the LEU2 gene.

TABLE 17 Plasmid stability of pSAC35-based vectors containing arecombinant transferrin gene and the S. cerevisiae PDI1 gene at theSnaBI/NotI-site in the UL-region in strains DXY1 and DXY1 Δtrp1pdi1::TRP1. 10 mL YEPD shake flasks were inoculated with DXY1 [pDB3179],DXY1 [pDB3180], DXY1 [pDB3181], DXY1 [pDB3182], DXY1 Δtrp1 pdi1::TRP1[pDB3179], DXY1 Δtrp1 pdi1::TRP1 [pDB3180], DXY1 Δtrp1 pdi1::TRP1[pDB3181], and DXY1 Δtrp1 pdi1::TRP1 [pDB3182] were grown for 4-days at30° C., 200 rpm. Samples were spread onto YEPD-agar plates and grown tosingle colonies. Fifty randomly selected colonies were patched out inreplica onto BMMD and YEPD plates and incubated at 30° C. Plasmidstability was scored as the percentage of colonies able to grow on bothmedia. Plasmid Stability (% Prototrophs) SnaBI/NotI DXY1 PlasmidCassette DXY1 DXY1 Δtrp1 pdi1::TRP1 pDB3179 LEU2 rTf PDI1 56 0 100 → → →pDB3180 LEU2 PDI1 rTf 36 0 100 → ← ← pDB3181 LEU2 rTf PDI1 28 0 100 → →← pDB3182 LEU2 PDI1 rTf 15 0 100 → → ← * Arrows indicate the directionof transcription relative to the LEU2 gene.

DXY1 containing pDB3175-pDB3182 were compared with DXY1 Δtrp1 pdi1::TRP1containing pDB3175-pDB3182 for the secretion of recombinant humanalbumin and transferrin (N413Q, N611Q). FIG. 34 shows that followingdisruption of the genomic PDI1 gene with TRP1 to increase plasmidstability to 100% (Table 16), there was a reduced recombinant humanalbumin titre for PDI1 inserted at the SnaBI-site. However, this is morethan compensated for by the increased genetic stability followingdisruption of PDI1 in the genome, which increases the reproducibilityand reliability of heterologous protein secretion, resulting in a moreuseful industrial organism for application in consistent proteinproduction, especially in prolonged cultivation, such as fill and drawfermentation or continuous culture fermentation campaigns. Furthermore,when PDI1 was located at the XcmI-site after REP2 of pSAC35 (Example 12)there was no significant decrease in rHA titre following disruption ofthe genomic PDI1 gene with TRP1 to increase plasmid stability (Table13). This suggests that the XcmI-site was preferred (but not essential)compared to the SnaBI-site for PDI1 on 2 μm-based plasmids expressingrHA. However, PDI1 expression can be modulated, for example by alteringthe length of the PDI1 promoter (Example 7) such that an increase inrecombinant protein secretion is observed. In the above experiment thelong PDI1 promoter was used, which was not the preferred promoter lengthfor optimal rHA secretion in the closely related high rHA producingstrain, DS569, where a short promoter resulted in increased rHAsecretion. In the case of genomic PDI1 disruption in DXY1 [pDB2977]containing a long PDI1 promoter in PDI1 at the XcmI-site after REP2 ofpSAC35 (FIG. 19), the analysis included three individual isolates (nottriplicates of a single isolate as shown in FIG. 34), and demonstratedno decrease in rHA titre. Furthermore, the increased consistency andreproducibility is clearly demonstrated for these cultures followingdisruption of the genomic PDI1 gene.

In FIG. 35 a large increase in recombinant transferrin secretion wasobserved between DXY1 [pDB2931] without PDI1 on the pSAC35-based vector(which itself was not 100% stable), and strains containing plasmidspDB3179-pDB3182, with PDI1 at the SnaBI/NotI-site. In DXY1 Δtrp1pdi1::TRP1 containing plasmids pDB3179-pDB3182, PDI1 on the plasmid wasacting as the sole selectable marker and resulted in improved geneticstability (see Table 17) where 100% plasmid stability was observedwithout any decrease in recombinant transferrin secretion. Hence, byplacing PDI1 on the transferrin expression plasmid and disrupting PDI1in the genome, the overall effect has been to increase secretion of therecombinant protein and also to improve the genetic stability of theproduction organism

1. A method for producing a desired protein (such as a desiredheterologous protein) comprising: (a) providing a host cell comprising afirst recombinant gene encoding a protein comprising the sequence ofOrm2p or a variant or fragment thereof and a second gene, such as asecond recombinant gene, encoding a desired protein (such as a desiredheterologous protein), with the proviso that the first and second genesare not present within the host cell on the same 2 mm-family plasmid;and (b) culturing the host cell in a culture medium to obtain expressionof the first and second genes.
 2. A host cell comprising a firstrecombinant gene encoding a protein comprising the sequence of Orm2p ora variant or fragment thereof and a second gene, such as a secondrecombinant gene, encoding a desired protein (such as a desiredheterologous protein), with the proviso that the first and secondrecombinant genes are not present within the host cell on the same 2mm-family plasmid.
 3. A method according to claim 1 wherein either orboth of the first and second genes are located on a plasmid, andoptionally located on the same plasmid.
 4. A method according to claim 1wherein the first recombinant gene encoding a protein comprising thesequence of Orm2p or a variant or fragment thereof is located on aplasmid.
 5. A method according to claim 1 wherein either or both of thefirst and second genes are integrated into the chromosome of the hostcell.
 6. A method according to claim 1 wherein the first recombinantgene encoding a protein comprising the sequence of Orm2p or a variant orfragment thereof is integrated into the chromosome of the host cell. 7.A method according to claim 1 further comprising the step of purifyingthe thus expressed desired protein (such as a desired heterologousprotein) from the cultured host cell or the culture medium.
 8. A methodaccording to claim 8 further comprising the step of formulating thepurified desired protein (such as a desired heterologous protein) with acarrier or diluent and optionally presenting the thus formulated proteinin a unit dosage form.
 9. A plasmid comprising a first recombinant geneencoding a protein comprising the sequence of Orm2p or a variant orfragment thereof and a second gene, such as a second recombinant gene,encoding a desired protein (such as a desired heterologous protein),with the proviso that the plasmid is not a 2 mm-family plasmid.
 10. Amethod according to any claim 1 further comprising an additionalchaperone protein or variant or fragment thereof, or gene encoding anadditional chaperone protein or variant or fragment thereof.
 11. Amethod according to claim 11 wherein the additional chaperone isselected from PDI1, JEM1, AHA1, CCT2, CCT3, CCT4, CCT5, CCT6, CCT7,CCT8, CNS1, CPR3, CPR6, EPS1, ERO1, EUG1, FMO1, HCH1, HSP10, HSP12,HSP104, HSP26, HSP30, HSP42, HSP60, HSP78, HSP82, MDJ1, MDJ2, MPD1,MPD2, PFD1, ABC1, APJ1, ATP11, ATP12, BTT1, CDC37, CPR7, HSC82, KAR2,LHS1, MGE1, MRS11, NOB1, ECM10, SSA1, SSA2, SSA3, SSA4, SSC1, SSE2,SIL1, SLS1, UBI4, ORM1, ORM2, PER1, PTC2, PSE1, HAC1 or truncatedintronless HAC1, TIM9, PAM18 or TCP1 or a variant or fragment of any oneof these.
 12. A method according to claim 1 wherein the desired protein(such as a desired heterologous protein): (i) comprises a leadersequence effective to cause secretion from the host cell, such as yeast;and/or (ii) is a eucaryotic protein, or a fragment or variant thereof,optionally a vertebrate or a fungal (such as a yeast) protein; and/or(iii) comprises a sequence selected from albumin, a monoclonal antibody,an etoposide, a serum protein (such as a blood clotting factor, e.g.Factor VII, Factor VIII, Factor IX, Factor X and Factor XIII),antistasin, a tick anticoagulant peptide, transferrin, lactoferrin,endostatin, angiostatin, collagens, immunoglobulins, orimmunoglobulin-based molecules or fragment of either (e.g. a dAb, Fab′fragments, F(ab′)₂, scAb, scFv or scFv fragment), a Kunitz domainprotein, interferons, interleukins, IL10, IL11, IL2, interferon aspecies and sub-species, interferon b species and sub-species,interferon g species and sub-species, leptin, CNTF, CNTF_(Ax15)′,IL1-receptor antagonist, erythropoietin and erythropoietin mimics,thrombopoietin and thrombopoietin mimics, prosaptide, cyanovirin-N,5-helix, T20 peptide, T1249 peptide, HIV gp41, HIV gp120, urokinase,prourokinase, tPA, hirudin, platelet derived growth factor, parathyroidhormone, proinsulin, insulin, glucagon, glucagon-like peptides,insulin-like growth factor, calcitonin, growth hormone, transforminggrowth factor b, tumour necrosis factor, G-CSF, GM-CSF, M-CSF, FGF,coagulation factors in both pre and active forms, including but notlimited to plasminogen, fibrinogen, thrombin, pre-thrombin,pro-thrombin, von Willebrand's factor, a₁-antitrypsin, plasminogenactivators, nerve growth factor, LACI, platelet-derived endothelial cellgrowth factor, glucose oxidase, serum cholinesterase, aprotinin, amyloidprecursor protein, inter-alpha trypsin inhibitor, antithrombin III,apo-lipoprotein species, Protein C, Protein S, a metabolite, anantibiotic, or a variant or fragment of any of the above.
 13. A methodaccording to claim 13 wherein the desired protein (such as a desiredheterologous protein) comprises the sequence of albumin or a variant orfragment thereof.
 14. A method according to claim 13 wherein the desiredprotein (such as a desired heterologous protein) comprises the sequenceof a transferrin family member, optionally transferrin or lactoferrin,or a variant or fragment thereof.
 15. A method according to claim 13wherein the desired protein is a desired heterologous protein thatcomprises a fusion protein, such as a fusion protein of albumin or atransferrin family member or a variant or fragment of either, fuseddirectly or indirectly to the sequence of another protein.
 16. A methodaccording to claim 1 wherein the host cell is a eukaryotic cell such asa yeast cell, optionally a member of the Saccharomyces, Kluyveromyces,Arxula, Yarrowia, Candida, Schizosaccharomyces, Debaryomyces,Xanthophyllomyces, Geotrichum, Ashbya, Hortaea, Schwanniomyces,Trichosporon, Xanthophyllomyces, or Pichia genus, such as Saccharomycescerevisiae, Kluyveromyces lactis, Pichia pastoris, Pichiamembranaefaciens, Zygosaccharomyces rouxii, Zygosaccharomyces bailii,Zygosaccharomyces fermentati, Kluyveromyces drosphilarum, Pichiamethanolica, Hansenula polymorpha (also known as Pichia augusta), Arxulaadeninivorans, Yarrowia lipolytica, Candida boidinii Candida utilis orSchizosaccharomyces pombe.
 17. A method according to claim 1 where, whena 2 mm-family plasmid is used: (a) the plasmid is based on pSR1, pSB3 orpSB4 and the host cell is Zygosaccharomyces rouxii; (b) the plasmid isbased on pSB1 or pSB2 and the host cell is Zygosaccharomyces bailli; (c)the plasmid is based on pSM1 and the host cell is Zygosaccharomycesfermentati; (d) the plasmid is based on pKD1 and the host cell isKluyveromyces drosophilarum; (e) the plasmid is based on pPM1 and thehost cell is Pichia membranaefaciens; or (f) the plasmid is based on the2 mm plasmid and the host cell is Saccharomyces cerevisiae orSaccharomyces carlsbergensis.
 18. A method according to claim 1 in whichthe plasmid is based on the 2 mm plasmid and the host cell isSaccharomyces cerevisiae or Saccharomyces carlsbergensis.